I want to use gedit as a programming IDE and as a regular text editor. Would I be able to make some .desktop file to load a different configuration?
It doesn't seem to be supported right now, see this upstream bug report.
However, you could create a wrapper for gedit, that sets the specific plugins you want via gconftool-2.
This would look something like:
Now save this somewhere as eg. gedit_profile and make it executable:
To load different profiles, just call it with a comma-separated list of plugins you want to enable, for example:
[Of course you then can put this into separate launchers.]