I found a sweet deal on a slightly used Aimpoint CompM2. Will it co-witness with any of the carry handles or flip up rear sights RRA offers?

As long at you use the right mount.

What Jack said.
It all depends on where and how you want to mount it.
Steve/RRA

Quoted: I found a sweet deal on a slightly used Aimpoint CompM2. Will it co-witness with any of the carry handles or flip up rear sights RRA offers?

I have one mounted on my Rock River Arms UTE and the sights co-witness with the red dot.  The UTE has a knurled piece on the right side of the upper receiver that covers a place to store an extra Aimpoint battery.  It works great.  

yes but what MOUNT are you using?  

PBR Sailor is apparently using the original UTE upper with an extra wide, low ring...probably the one that Aimpoint used to include with the optic.
Most of the mounts on the market are made to offer co-witness from an A4 upper receiver.  That said, every mount I've meaured is slightly different from from those of different manufacturers.  The Aimpoint QRP ring with the optional spacer provides a very reasonable co-witness from a flat-top receiver with normal front sights and any number of optional rear sights, both flip-up and stationary.  I've got mine forward mounted with 22M68 rings on ARMS 38SXL Swan sleevesthat have an integral flip rear sight.  Other folks use goose neck mounts off of an A2 carry handle.  You'll need to define your requirements a little bit in orderfor anyone to make a solid recommendation, but suffice to say that there is a mount out there that will work for your needs.
Steve/RRA