While it's pretty unlikely that your ETA checked during your trip through NI, or that you would be stopped at all, it's probably not worth the risk. If you were to get in an accident or come upon a random UK border control check, it could lead to unnecessary trouble and delays. The ETA is pretty cheap and easy to obtain, but if going to that trouble you should probably take a side trip to see some of the sights of Northern Ireland. For example, driving up to Coleraine and taking the Loch Foyle ferry is a fantastic way to enter Donegal, and leaves you a stone throw from Malin Head, the most northerly point on the island.
Alternatively, you could make a stop in Sligo before entering Donegal from the south, avoiding the need to pass through NI at all.