Drone autopilot for logging position and orientation?

We're doing aerial photography for monitoring surveys of large mammals - but our 'drone' is actually a crewed Cessna or microlight with oblique cameras on the wing struts. Currently using a raspberry pi with IMU and external GPS but there are a number of issues with time synchronisation and ensuring logging starts correctly.

Developing v2 of the system and would like a better solution for logging the angle of view of the camera (i.e. IMU / GPS data). Ideally I'd be able to log angle/acceleration data (IMU), GPS (XYZ) and camera-trigger events (hotshoe of camera) to an SD card. I'm thinking about using a Pixhawk autopilot, since that should log GPS and IMU data automatically, and power needs are simpler (USB input).

However, I'm concerned about how difficult it would be to configure the autopilot to 'arm' and start logging at the beginning of a session, since it's not connected to motors or servos. 

Is this a suitable use for a drone autopilot or should I be looking elsewhere?