I am seeing that you can launch FaceTime from your app via
[[UIApplication sharedApplication] openURL:[NSURL URLWithString:@\"facetime://tel-number\"]];
I don't see any reason this would be rejected, especially if there's already an app that uses this functionality. The App Store Review Guidelines are the best way to determine if your app will be rejected, and I don't see anything in there that applies to you situation.
Of course, Apple can do whatever they want, so the only way to be absolutely sure it will be accepted is to submit it, but I highly doubt you will have a problem.