Debugger with Breakpoint and Variable read/set capability
There is something quite close to what you are asking.
You need either the (more expensive) ICEMKII (iirc) or the (cheaper) AVRDragon.
Then it's possible to use it with gdb.

In practice the AVR supports only one breakpoint, so what happens is that the binary in flash will be dynamically patched.
This will slightly reduce the life of the AVR, but I think it's fairly acceptable. One can always use Arduino UNO with the original DIP package for AVR, mounted on a socket. Then it's sufficient to replace the burnt microcontroller and keep the rest (but it's hundreds of thousands of programming cycles before the AVR fails).