FWIW, the way people usually hack the editor themes right now is something like this:
This is a fairly harmless but pretty tedious and fragile method (it breaks every time you update the RStudio IDE). And your options are somewhat limited by the way Ace editor themes work (they’re pretty much ports of TextMate themes), so you can’t easily do things like have the Markdown in R Markdown documents be a different font from the code chunks (that would be a top feature on my list!).
I believe the IDE team has stated that they want to make an officially supported method for people to customize editor themes, but it hasn’t made it into a release yet.