Thank you for your feedback. I'm glad you enjoyed the game.
I noticed this bug as well yesterday while I was de-spaghettifying the code. It seems I was resetting the number displayed at the top upon restarting, but not the actual internal flag count. It'll be fixed in v0.2, thanks for reporting it.
As for an alternate camera control like that, I hadn't thought about it. In my experience it gets tricky to navigate tight spaces with controls like that (in programs like Blender), but I suppose most of the levels here don't have that. I thought a while about what control scheme would work best, and I think something like what you described would work best:
Camera is stationary by default, and any tile in view can be clicked. Holding right mouse lets you spin the camera around some orbit point (initially at the center of the level). Holding middle mouse lets you pan the camera perpendicular to its view direction, which also moves the orbit point. Scroll wheel would allow the camera to move closer to or farther away from the orbit point. This can be combined with the flight movement for finer control if need be.
Does this sound good?