Most head units will put out to two and four-ohm speakers. Just at different wattages. I added Rockford Fosgates all the way around and kept my stock tweeters as well, It's been almost a year and I haven't had any issues.
While you're hooking up your wires to the new harness for the head unit, I would just leave the rears off of the harness as well, just to prevent a short in the future.
Next, get some small wire caps/crimps to put on the wires if you're going to hook them up. They wont come off like tape will in warm weather. You can buy a pack at any automotive store for like $2.
2001 SLT, Reg Cab, 3.9, 4x4, Auto 42RE/A500
USAF Rigger OEF Vet