Honestly, I think it's just fine. Lots of people have done it in the past, lots of people do it now, lots of people will do it in the future.
It can wear differently than 100% cotton, so over the years it may become increasingly obvious which squares had the poly blend (they're generally more durable and stays brighter colored), but that's really all I think anybody should need to worry about for a quilt. If you keep the entire quilt consistently a poly blend that solves that issue.
I actually prefer poly blend for pet quilts. It's just that much more durable.