MakerBot based machine and Reprap based machines split years ago and therefore are NOT compatible.
Repetier can create mostly compatible gcode but cannot control the bot.
There are not Reprap Firmwares ported (marlin and varriants such as Repetier)to Makerbot electronics.
The ressons are quite complex, but it comes down to pin wiring and chip choice (say the thermocouple temperature measurement system used on MakerBots) so you cannot just willy nilly configure the pins and port it from one board to the other.
Your best bet is to run Sailfish and you could use GPX, a converter to take raw gcode and export it to X3G format consumed by makerbot firmwares.
You also should know that controlling the BOT by USB is very bad, there have been some major bugs in the underlying protocol and error handling and Sailfish has huge warnings about this. Note that stock firmware has the same bugs, but user fly completely blind to the errors that are happening in the background. In short, ALWAYS print from SD card and basically the GPX converter will allow you to convert gcode produced by Repetier or any of the other major slicer programs and print from SD card.
The other option is to buy RAMPS or RAMBO control boards and also replace the thermocuples with thermistors, replace all the connectors, and basically rebuild the bot using Reprap control and wiring.
Most of us techs run Sailfish and are happy. I run Repetier on my Rostock MAX, but hands down, I prefer Rep-G with Sailfish.