It might be possible to use Slic3r
http://slic3r.org/blog but then we have to go down the road that your MakerBot Replictor 2 ONLY understands X3G files, not straight gcode and that now you must use GPX to then convert the gcode created by Slic3R to X3G so your MakerBot can read it.
https://github.com/whpthomas/GPX
In order, you must get the following right:
You must ensure Slic3R is generating compatible gcode language and commands that can even be understood by GPX
You must use GPX to then convert to X3G
You must print using SD card.
Supposedly, this has a little more integration and GPX defaults to a Replicator 2 with no other configuration statements so you have that going for you but I had trouble finding a recent tutorial on that exact setup with a Replicator2.
best of luck.
This is why the $140 price tag of S3D starts becoming really attractive when you calculate how much time you waste trying to get other "free" tools to work.