We've spoken with a number of Cypriots and expats and they've told us:
1) As a visitor, it's 'worse' to arrive Ercan and then depart from Paphos or Larnaca. You can do it, but the immigration officials at the latter will give you grief for making an 'illegal entry' into Cyprus. They COULD ban you from coming back. But no one has heard of that actually happening.
2) Departures from Ercan are not tracked/stamped - instead you get a stamped piece of paper (sort of like Israel does). So there's no evidence you made an 'illegal exit' from Cyprus.
3) In fact, many expats seeking residency exploit this. They fly into Paphos or Larnaca and get stamped in then make round trips out of Ercan. As far as Cyprus knows they were in Cyprus the whole time counting toward their stay-days for permanent residency.
Not sure what we'll do yet, but it appears to be pretty common for folks to fly into Paphos or Larnaca and then out of Ercon.