Probably the best way to do this is to construct the full query yourself and then use the standard getArrayFromUri:
method. Taking your example, this would look like:
FatFractal *ff = [Store ff];
NSString *query = [NSString stringWithFormat:
@"%@/messages?sort=createdAt desc&start=0&count=1",
[ff metaDataForObj:thread].ffUrl];
NSArray *result = [ff getArrayFromUri:query];
For more info, see http://fatfractal.com/prod/docs/queries/#sorting-and-limiting-results.