They don't make replacement towers but if it's really bad ( I have seen some) you would cut out a tower section from a junk car and weld/graph it in, a job for pro's.
Very true, it really is a job for a
pro.
Depending on the location of the rust and the amount, it would be hard to fix the shock tower with the engine in. But, not impossible! Again, it depends on
where exactly the rust is.
For example, I folded and welded the back portion of my strut tower to fit in my booster. That was with the engine in the car. But, obviously, no booster or other stuff in that area.
http://www.veryuseful.com/mustang/joe/brakes/graphics/bumpForPowerBooster2.jpg
You may be able to get to it by just taking off the wheel, using some sandpaper to clean up the area, and put a patch on from there.
If it's minor (which it sounds like), then you're really doing a
cosmetic fix and to prevent any further rusting. In that case, I suggest using epoxy putty. You'd make a "plug" that went over both sides. You'd want at least 1/8" think in the engine bay, and then 1/4" to 1/2+" think in the wheel well (where it wont show as much).
Note: Regardless of the BS that you may have read, the strut towers FLEX A LOT! That's been know since the 50's! Strut tower braces are not new. So, if the hole is too big, then the non-flexing epoxy patch isn't a good idea.