Yes, it's not like ATC are suddenly going to start installing every random nightly release on their production systems.
I would imagine they would stay safely (maybe even years) behind the cutting edge. But common availability of the source code would make it easier to share information that may be able to speed up acceptance testing or flag up issues.
You could argue it's actually more dangerous for an airport to rely on software that is opaque, for all they know there is some edge condition in there by accident (or on purpose) that could cause mayhem.
I am going to assume however that ATC software source code is rigoursly audited by a trusted partner of the airports using it.