Cool! We use this but never had too much problems with disk usage (I/o or size). But, were only using to deploy configs across multiple nodes. And we read the local copy directly!
I would -imagine- that 'slight staleness' won't matter for your use case (I'm pretty confident that for the sort of configs I'm considering rqlite for that'll be the case, at least) but it's probably worth triple checking when configs are involved.
Can you expand a bit more on your concern? What scenario do you have in mind?
I could easily be imagining a problem that won't exist.