I think that it was actually more cost-effective for them to procure their own parts, I seem to remember one journo blog recently backing this up relatively recently, pointing to the fact that GP2 suffers due to the relatively high cost of new parts when procured via Dallara.
If memory serves, they damaged the parts during a race weekend, and thought that if they sent them back to Dallara, they wouldn’t get new parts in time – it may have been during a GP2 Asia race – so they decided to fix the parts themselves and complete the race meeting.
Anyway, if Coloni have been done in for a technical infringement that could be classified as cheating, then it is probably something they have been doing all season, and may feel that it is not technically illegal, and that is te source of the disagreement. The series organisers have stripped them of their points and will take any further points from them, but they haven’t publicly kicked them out. So Coloni have interpreted the rules one way, the organisers have said no, but have understood how Coloni could have come to that conclusion, and so allowed them to bow out with their dignity (relatively) intact.