I believe she can still get her ILR even if you are working away. I wouldn't say it's permanent though and I presume you would be able to come back occasionally?
Seems a shame for her to miss out on getting a passport when she's not so long to go - who knows what the future holds?
If she does stay she needs to go the 'whole hog' and get citizenship and a passport - ILR alone may not be enough. See this thread: