I'd much rather pay Millsap than Noel given Noel's injury history, off court issues, and his seemingly never ending comments about how unhappy he is. Remember this a guy that is a free agent this summer and has played in just 8 games averaging less than 12 mpg thus far this year. This after missing 15 games last year. His rebounding rate is way down, though it is such a small sample it is hard to put much faith in it.
That said, Noel will likely come cheaper than Millsap and thus there may be more value to the team in acquiring him as opposed to paying more to acquire Millsap. But make no mistake Noel is a horrid offensive player who can basically just dunk and thus far this year isn't rebounding or defending particularly well (though I would expect both of those to increase as he gets healthier).
The surgery was elective, and from what I've gathered it was pretty much due to the major logjam that the Sixers had. The Sixers wanted him to do it to provide them more time to evaluate Embiid and Okafor at the beginning of the season, and he kind of just went along with it.
And it's hard to evaluate Noel's true injury history. Yes, he tore his ACL in college, but that's seemingly never been a problem for him in the pros. He played 75 games his rookie year, and last year he played 67. However, with how the Sixers have blatantly embraced tanking in his tenure, along with the issue of the logjam last year and this year, there's no telling how many of those games he was held out of in order to tank. Hell, that's exactly what happened in his "real" rookie year. He could've came back several months before the end of the season, but the Sixers didn't want to win any extra games or chance him injuring himself again.
I think his injury history is largely overblown. He'd easily be the most athletic big we've had in a long while.
If he got around 16-18 for four years, which seems about right for his value right now, wouldn't you prefer that to a four year deal of around 24-25 for an aging Milsap, whose game will certainly not age all that gracefully?