No, that would be a solution which would say: Don't bother even if you know that the Pokemon was hacked, you can buy it, keep it for a few months then sell it for twice as much. This solution would encourage players to help hackers by buying their Pokemon, and to look for hacked Pokemon as their value will double up in a few months so they are great investment.
Giving back the hacked Pokemon would make a very dangerous precedent. It would create a legitimate market of hacked Pokemon with huge demand and thus huge possible profit for the hacker. The buyers would lightheartedly buy the hacked Poke because they know that they wouldn't lose it so for them there is no risk, but they will get a valuable Pokemon whose value will increase once the hacker is caught and the Poke becomes unavailable once again.
And what would this mean for the events? "A new Pokemon became catchable? Oh well, why would I bother hunting that HR for the next two weeks when I can get it for 2m on the illegal market and I don't even risk it to lose my investment?"
Hacked Pokemon should be deleted. THos who bought them already have their Pokedex data, and they should get some other compensation, bu definitely not their hacked Pokemon, which will worth much more than they paid for them once this whole case is solved.