They had no idea why Luffy was there. It's not like Luffy's relation to Ace was public knowledge.
Your argument sound like you're faulting Magellan for not realising that Luffy is the main character and doing everything in his power to stop him early.
The bolded is irrelevant. Magellan swore that he would not allow Luffy to rescue Ace, nor would he allow him to step outside of Impel down. It doesn't matter what kind of relationship he has with Ace, he swore that he wouldn't let him get away for breaking inti impel down.
I'm not 100% on Stat's side here (he basically killed Luffy, and I don't have a problem with his actions regarding the way he dealt with him). He had no way of knowing that Luffy would be saved by Ivankov (who was presumed dead.)
I just thought it was odd that a man (who basically kills prisoners on a whim for insulting him) would let Mr. 2 live, considering it was because him Luffy managed to escape with his life.
It's quite possible that Blackbeard freed his new crew in time to interrupt Megallan from wrecking Bon Clay proper.
Err you mean Shillew right? I definitely agree this is probably the only possible answer here.