Are there any critical drawbacks of rendering animation on per frame basis? I have a scene, where rendering is controlled by python script which takes a still image on each frame. After test run I can't name any "problem" except inability to abort rendering without crashing Blender.

Will animation output (image sequence) be the same as with default "Animation Render" or it's not that easy?
No, if you render all your frames individually the result will be the same of pressing "Render Animation". This button is only iterating over all frames and sending the render command for each of them.

As for the render crash, you could use a modal operator that checks if you press Esc (for example) and aborts the render without making Blender crash