We tend to have quite a bit of freedom with what we choose to do in any mission (which is probably a part of why we're so choosey about who gets Permission); the general rule is, if it can still affect canon, get rid of it. Jay and Acacia wrote that if a Mary Sue dies without any help from us, her 'legacy' will continue to affect tha canon characters.

If the child is a miscarried foetus, you don't have to do anything - let it die. If she goes through the issue that quick it's clearly not important to the story. The Sue herself is obviously the main source of un-canon-ness, so I'd say the pregnancy is effectively the same as if she'd described a rather odd-looking pillow in the Hogwarts Great Hall - it'll vanish, without a trace, once she's gone. (What you need to be most careful of are the things your agents bring in with them; they cannot be left behind.)

As for the garden, it's your call. If your agents are feeling particularly angry, let them burn it down, but be aware that canon characters might see the smoke. Use your best judgement.

(Also, "kids" should be "kid's" - yes, I'm picky, but this is the PPC; it's my job ;) )