I see your point about not wanting to be tied into a set routine. But you need to think about the messages that MIL is getting from this.
What she will understandably be hearing is....
I don't want to be tied to a fixed routine. But I will do for nursery because his relationship with nursery is important. I won't do it for you because. His relationship with you isn't as important
I value nursery's input into his life so much that I want him to still go there. I don't value your input into his life that much
Because nursery is so important in his life, in fact irreplaceable, and because I completely understand that they have other demands so they can't guarantee that they will keep his place open for him if he isn't using it, I will continue to send him. However MIL I expect you to remove all other demands on your time and hold a place open for him whether I use it or not. And actually because you are not that important in his life, I will easily replace you if you don't
Those may not be the messages you intend to give to her, but whether you intend it or not they are coming over loud and clear to PPs and probably to your MIL. As such you are being (probably unintentionally) ungrateful for what your MIL does for you and not really valuing it.
I understand that you say she will still see him at weekends, but in saying that the message your MIL is likely to (understandably) hear is that you don't value the time and commitment she puts into providing childcare nor do you see the importance of her having, and maintaining, a one to one relationship with your DS.
Surely you can understand how such messages -intentional or not - would be rather hurtful? And how somebody who has been made to feel like the favour they are providing isn't valued, might be tempted to say "I'm not doing it any more then"?
I completely get that you want some time with your children. However I think you also need to be fair to your MIL. If you can be in a routine for nursery you can be in a routine for her. If you can acknowledge the importance of keeping your DS's routine/relationship with nursery, then acknowledge the importance of his routine/relationship with her. If you can understand that nursery would be reasonable not to hold that space free for him if he wasn't going, then be equally understanding about your MIL.
I think you need to try to work out some compromise here. Your MIL isn't a paid service that you can book when you want to and not when you don't. She's doing you a favour, and favours have to be reciprocal. Could you -for example - continue to pay for two days a week at nursery but on the week he goes to your MIL's only send him to nursery on one of those days? Or could you agree with MIL that instead of every fortnight, she could have him one day every three or four weeks?
I'd also say be careful about cutting down childcare options before you see what your new baby, and life with two children, is like. If you have an easy birth and a placid baby you may well find it easy to look after both at once. If you have a difficult birth or a baby who is up all night you may well be very glad to know that every Thursday you can drop DS at grandparents so you can sleep when your baby sleeps.