I had the same concern. I was tempted to try to get my HOTAS controller setup to work like OP described, but, I ultimately didn't think it was worth the risk of a false flag from the anti-cheat detection.
I understand banning people who abuse external software for an unfair advantage - in fact, I fully support those kinds of bans. But, I'd really love to be able to fly some of the vehicles with an actual stick and throttle. I've tried with mouse and keyboard on occasion, but I've been a liability to my team each time I've hopped in as a pilot. Maybe having a regular gamepad plugged in and ready is the interim solution. This is slightly unrelated to the main point of this thread, but, some sort of 'firing range' test area for vehicles would be awesome, too - to be able to get a bit of practice in before taking one of the limited jet/heli spawns in a multiplayer match.
In any case, official multi-device joystick support (i.e., stick, throttle, and even rudder pedals) - or at least a statement explaining whether or not the DIY route is sanctioned, in the meantime - would be incredible.
I'll echo the sentiment, as well: fantasic release, I haven't had this much fun with a FPS in a long time. Reminds me of some really fond memories of Bad Company 2 and BF3.