In my experience, if you're perplexed by someone's behavior, it's almost always good to pose a direct question. Of course, it's important to actually ask a question, rather than make
an accusation in the guise of a question. You might ask your mother-in-law how it is for her when you leave her alone, for example, and whether there's anything you can do to make her more comfortable in your absence -- as opposed to saying something like, "Why do you guilt trip us whenever we go out?"
When you say she makes you feel guilty, how does that work exactly? Does she look sad or does she call you selfish and self-centered? She can only make you feel guilty if you're already part way there. If she looks sad, then you'll have to try to accept the fact that she is entitled to her feelings, and give yourself permission to have needs which conflict with hers -- which is true in all relationships.
It's important for you and your partner to have private time together, even if your mother-in-law isn't happy about it. Remember, it will benefit her in the longrun if you and your partner maintain a strong relationship, and if you take steps -- like having regular times out together -- to nurture your relationship; this will also help you both avoid caregiver burnout. If your mother-in-law attacks you, then you need to make it clear to her that this behavior is unacceptable.
What are the consequences of your mother-in-law making you feel guilty? Does it get you to change your plans? I ask because if your mother-in-law has come to believe that she can control you then you may inadvertently be reinforcing the very behaviors you wish to stop.
I'm also wondering about the bigger picture. How was the agreement made to have your mother-in-law move in? Are you and your spouse and/or children all on the same page? You might want to consult with a family therapist for further guidance.