There aren't that many common blue lancers in Arena to begin with. Ephraim and Abel maybe, of which only Ephraim was a bonus unit. Catria is there but she gets shut down by Takumi anyways so she's irrelevant.
On the other hand, next arena season will likely feature the blue tome siblings and frobin as bonus units so we'll likely be seeing quite a few people pulling their robin up to 4* for that Gronnwolf (plus Ursula grand hero battle)
I'd be pissed if they banned rooted phones. It's the main reason I haven't paid in any money because I don't want to dump 60 bucks and then get banned for using a rooted phone.
The much less anti-root method would be to do sanity checks on the server end. The game only connects to the server at the start and end of each battle right now anyways. Log what happens during the battle and send it up to the server. If anything smells funky, revert their state.