Really the only difference between relational stuff in an SQL database and a relational library on top of Mongo is that SQL has years and years behind it. It's only a matter of time before these newer DB's have solid built in relational stuff or community libraries built on top of these DBs that are just as solid.
It's just code, you don't have to stick it in your app, you can stick it in an NPM repo and encourage contribution from the community, and make it a re-usable library.
The requirement of having transactions in an app doesn't determine if meteor is good or not. Meteor is quite great at what it does, but it may not have absolutely everything that you need.
That's what tools are about: picking the right one for your requirements. :}