Basically what it says in the title, MechJeb would need to burn reterograde to do this. I don't think that that feature's particularly hard to code.
Thanks!

MechJeb is already able to set up retrograde burns with the maneuver planner. Probably you are asking it to do something physically impossible and it is complaining. If you are in a 300km circular orbit and ask it to change the periapsis to 200km, it will set up the proper retrograde burn. If you are in a 300km circular orbit and ask it to change the apoapsis to 200km, it will complain because it is physically impossible to do that in a single burn.