It may be possible, but I don't think I would do it...
I own a Probe GT actually, and as I've mentioned before, I've had lots of problems with the car over the years. I autocrossed the car before, so that might contribute to a bit of wear, but let me see...
It was a daily driver, now with 177,000 kms on it. I never modded the engine itself, only intake, exhaust, ignition, and various small stuff. On the odd time I drove it pretty hard, but otherwise I'm no maniac and don't launch the car at every stop light or anything, and neither do I redline the car (I've done it a couple times over the years only...surprising?)...
'93 Probe GT, major repairs till now - engine gaskets blown twice (oil leaks), actually a third time as of now, I think...oil's coming through the sparkplug holes...distributor blown twice (damn pricey part), stock sparkplug wires frazzled, ECU problem, had to replace (stock one). Engine was replaced

once, due to (I forgot) but something blown in the bottom end, causing oil to gush unknowingly during one trip, and fried the bottom end.
Minor repairs unrelated to the engine included too many things to mention, but stuff like the 2nd gear blew up after 5 years (OK that's sort of not too bad, but still...), oil gauge was never accurate, replaced 5 times (!!), 02 sensor replaced a couple times, timing belt snapped once (that was due to engine oil leaking on it and screwing up the belt's material), and various failures for emissions tests (after about 5 years of owning the car).
So, I'd be careful about putting in an old Probe engine into the MP3. Maybe I was one of those unlucky ones, but I'm pretty sure I'm not the only one. Then again, a fellow with an MX6 in another post claims there were no problems with his car, so who knows? All I'm saying is be careful...