For a ‘forced layup’ shot you will have a negative SG, but this is a better choice than taking a driver and hitting into trees or worse trouble. This is a situation where the SG for a given shot is not as accurate as it could be. However, if you track your results over time at this course, overall changes will indicate progress.
The only other ‘solution’ is to ‘artificially’ increase the hole length. This would change the SG (but would also incorrectly factor into the drive distance standard statistic).