The only thing that I can think of is that they think this will lead to a constitutional amendment which will disallow any public funds going to private school students.
(Either that or there are some skeletons that they dont want disturbed - but I'll leave that conspiracy for FAA)
Some other possibilities
A) If it wouldn’t have gone in their favor it could have negative effects
B) They are happy with the lawsuit but don’t want the Commissioner upset at them so they need to show it’s not coming from them
C) The Commissioner can cause harm in other areas despite the good here
D) They have personal reasons to want to keep the status quo at the expense of the taxpayers