I don't get on v.well with my MIL either, I would never dream of having her look after either of my two, but frequently leave them with my mum....my MIL has never questioned this, I ued to feel bad but she sees the kids regularly and has 2 other grandchildren who she looks after quite often so I don't worry about it....MIL is wierd and getting worse, I'm just protecting my babies!
Just do whats right for you and your little one, maybe you'll change your mind maybe not - don't worry about it now though!