There was some work on a GraphViz replacement that you might be able to use: viewtopic.php?f=9&t=4742
The patches are probably out of date a bit, but could be relativley easily adapted. It was incomplete, though, so not yet committed so SVN.
You can also comment out the #include "gvc.h" and the entire contents of TechTreeWnd::LayoutPanel::Layout in TechTreeWnd.cpp to get it building, though you probably won't have a usable tech tree in game. I also haven't tested this, so it might cause a crash. If it doesn't crash, there is a clunky tech list, though, so it might still be possible to research techs.
Edit: looks like several other bits of TechTreeWnd.cpp would need to be commented out as well...
Edit: the attached patch might work. It removes all the graphviz dependence, at the cost of not having a visible tech tree. A more usable patch will require significantly more work.