It is possible for them to stop my licence application in such a situation?
It's actually muuuuch easier than that - because in Poland, the points are linked to the PESEL, rather than the licence - just go to the police station, own up and they'll deal with it there and then. How the hell did you manage to get caught by a camera in Poland, though? I mean, the big blue signs... :P
Shouldn't be a problem with the licence - the only issue is that the police might want to see the original licence. Actually - thinking about it - you might get an extra 50PLN fine if you aren't able to produce the licence. But - that, I'm really not sure about - there must be something allowing you to drive while in the process of exchanging a licence?
(bastard though - if you hadn't been in the process of exchanging the licence, your father-in-law could just blame some random "Christopher Bradbury" from the UK)