I'm not 100% sure, but it might work if you'll just delete everything from the repo folder and then create a TWS project in the same folder. Both TWS and Force.com IDE save sources under the 'src' folder, so Git should not lose the history if you'll just replace the files in the same folders. But when creating TWS project you'll need to uncheck the 'create directory for solution' or just manually move files accordingly to make the structure the same.
If your src folder is the root of the repository - you might need first to create the src folder and move everything there, so git will catch the move and then do the actions above.
So in general - there's no 'automated' way to do this from the IDE, however there should not be much problems with achieving the same results manually.
Hope this helps. Please feel free to get back to us if you'll have any additional questions or just let us know if everything works good :)