I can think of a way to have ballast that may meet both your objections to ballast (IE ruins the track, the mess). Here is my thought (my example uses a piece of gargraves 36" track, could work with any length of track, or you could use 3 10" pieces, etc)
1)Have a length of roadbed material cut to be the length of the track(s) you will be using) on a work area away from the layout (in my example 36"). I don't recommend doing a longer length than that, as will be seen moving that from the work area to the layout gets more difficult as the length increases, because you don't want to flex it.
2)Lay the section of track on the rubber roadbed, making sure to center it as best as possible, that it is laid straight as well (this might be tricky). If worried about shifting, you could use paper masking tape to hold the track in place on the sides/ends.
3)Ballast the track as you would if it was on the layout, use diluted glue, whatever to hold it.
4)Let it dry, at least to the point where the ballast is set enough not to move.
5)Remove the track piece. On the roadbed you should see the track profile outlined by the ballast you glued down
6)Secure the roadbed piece to your table, being careful not to flex it too much moving it (this is the one weakness of this, flexing it likely would cause ballast to fall off,maybe lay it on a 36" piece of wood to carry it over)
7)Lay the 'real' track you want to lay on the roadbed with the ties where the ballast isn't (basically when you are done, you shouldn't see any roadbed between the rails).
In a sense, you are creating pre done roadbed with ballast, sort of a distant kind of fasttrack and the like.
When creating the roadbed, you don't need to use sections of track to do the dirty work, you could create a jig easy enough using wood with the same profile as the track ties you are using cut to tie length for the track, and space them correctly for the track type and use strip wood nailed to the ties to hold it in the right alignment. I haven't tried this with track, but have done similar projects in other areas of modelling.
Another possible thing to try (I haven't, this is strictly something I thought of)
1)For roadbed, use something akin to the height of fast track or the like (relatively high),needs to be deeper than tie depth
2)Cut a piece of something akin to sandpaper (Sandpaper itself might work, with like 40 grit,but likely expensive), or the roofing material like the black mineral roofing roll HD has, it comes in a roughly 3' by 35" roll, which with let's say 5" wide roadbed, would give you roughly 6 pieces, and it is a little over a 1 a foot/6 pieces per foot. Cut the piece wide enough that it is the width of the top of the roadbed material + 2xdepth (so if the roadbed is 5" wide, and its depth is let's say 5/16, you would cut it 5 5/8" wide or so (it may be different if the roadbed is bevelled, you would need to calculate the width, or cut the piece wide then trim it)
So in my example of 36" section of roadbed, you could cut a piece 5 5/8"w x 36" long
3)Using spray tack or similar adhesive, glue the material to the top of the roadbed and to the sides as well, should totally cover it (trim any excess)
4)Using a section of track (or a jig with the ties spaced properly) laid on top of the material/roadbed, outline the ties on the material (trace around them).Make sure to align the track properly to the center line before doing this. You may want to secure the track with paper tape to keep it from moving.
5)Move the track aside, and using a hobby knife, cut the outline of the ties, going deep, and remove the roadbed material to a depth where the ties can fit nearly flush with the roadbed.
6)Put the track onto the roadbed, aligning the ties with the cutouts made through the material and press it down until the ties are down fully in the roadbed.
7)Glue roadbed and track section to the layout. Added benefit, no nails going through to the wood subsurface, will help reduce noise.
Because it has the material not just under the track, but the sides, it will look like there is ballast there. This probably would work better if the roadbed material has bevelled edges, but even if not but this would meet a lot of the criteria, won't hurt the track (added benefit, the track because it is 'sunk' in the roadbed can't move,you likely won't need nails), no mess and very little to no risk of the material having lose grit to clog engines and such. If you need to remove a section of track, it is pretty easy.
Both approaches will require finding roadbed that is easy to work with but especially in the second approach, is rigid enough to handle the track and not 'squish down' under the weight of the trains (cork would work, some stiff foams would work, might even be able to use insulation foam if you can find the right depth).
Like heavy floral wire. Solid copper. Etc.
Drill a hole(s) to overlap the edge of the edge on each side of a tie, and from under it, wrap up&over the tie, twist tight underneath.
One big hole used and looping thru a washer on the bottom will hold it there.
Zip ties are used along the same lines.
Removal of wrapping is just snip, snip, snip.
I've been playing with some thin plywood.
It was a drum alone on 2 long 2x4s stood 4"high as a base.
Two fairly flat, short nap terry towles over the 2x4s and the drumming was nearly gone.
I moved the towels to under the track and everything went silent.
I'm going to play with sandwiching a layer of cloth between boards.
The PITA is all holes will kneed to be known and predrilled and the cloth's hole cut or punched ahead of time; like a big gasket. (Can't drill cloth 
)
A diamond ringed spot weld cutter /grinder would do it if you have one kicking around (I did at times)
I'm really curious if the towel is stopping a bunch of reflective sound as well.
I have some dense rubber sheets to test a layer of too.
But I'm thinking two layers stacked and trimmed to fit into 0-27 ties, on 1/4" plywood, on cloth, on 1/4" plywood.
But I think silence is my goal. So if I have to I 'll use a short nap grey towel, a longer nap forest green one, tan pillow case and light brown fleece for ground cover.
I used thinner green foam on ply and it drummed. I layed a couple of tubes of rubbery foam adheasive down and it helped.
