Well, I know someone who was here as the spouse of an EU citizen, who was told by INIS that they would not renew her residency once her husband had filed for divorce - even though the actual divorce was still a long way off. So clearly they don't look purely at the technicality of the marriage.
I would think she'd probably be ok up until the expiration of her current permission, since these things are granted on a short-term renewable basis and changes in circumstances are usually dealt with by not renewing a status rather than automatically terminating it midstream. But she could still have a problem even when she gets to five years and applies for long-term residency, since the application itself doesn't confer a right to remain and she'd still need some underlying basis to be here during the processing period. Can she transfer to an ordinary work permit/green card, or apply for an indefinite permit on the basis of having worked for the same employer for five years?