Did "sublime" and "cherubim" rhyme in the past?
If you use the French pronunciation of sublime: /syblim/, and the Hebrew pronunciation of the -im ending: /-im/, they both rhyme with seem.
I very much doubt that's the way Edward Caswell intended you to pronounce the hymn.
Walker's pronouncing dictionary from 1828 says that sublime and cherubim were pronounced the same way then as they are today.
Most likely, this is just an eye rhyme:
Agreement in spelling, but not in sound, of the ends of words or of lines of verse, as in have, grave.
(Dictionary.com)