Do you have any trips, big projects, etc. coming up? There’s always the “We’ve got a big _____ coming up, and we need to start preparing/we’ll need more space for ___/we can’t have you staying here while we’re gone,” etc.
Even if you don’t, you could always pretend like you do. ;)
As @Jeruba and @Marina said, you could simply use a more tactful form of the question, such as “How long are you planning to stay?” or “When do you need to get back to your house? I could never leave my house unattended for so long.”
However, it seems like you need to talk with your husband privately and discuss the matter. You two need to be on the same page about the situation with your mother-in-law. There’s a fine line between visiting and imposing, and it seems to me that she has crossed this line. There may be something going on behind-the-scenes that would explain her long stay, and even so it seems she’s definitely overstayed her welcome. It’s probably time to give her the boot. You need to remind her politely that this is your home and although you love her visits, she simply can’t stay with you indefinitely.
In the future, make sure that your mother-in-law’s visits have specific check-in and check-out times to avoid more similar situations.