If you're planninng to install (the same version of) FreeBSD on the original server hardware, then rsync'ing back from the new system should be fine. But Debian<->FreeBSD is gonna be trouble in either direction.
But I'm specifically NOT talking about doing an rsync to get the data back.. the plan is to use in-protocol replication. Maybe that's a distinction without a difference, but that's why I brought it up.
The replication documentation, and more specifically the pg_basebackup documentation, makes no mention of cross-OS replication as being a problem for any reason. If that is expected to be a problem, then perhaps that should be updated?