This seems to be not the greatest idea. I tried it (by deleting all the conflicting files from torch5 before linking) and it didn't work. Well, Lua worked of course, but I couldn't load Torch, possibly because the Lua version (5.1.5) doesn't match up with the one Torch was going to install (5.1.3).

On the plus side, I discovered there is not actually a conflict with luajit, just lua (and presumably versions/lua52).