I think it should be fine to separate the larger ones, but just leaving the little ones attached at least until they form roots.
I currently have 30 inch tall ensete maureliis with 4-5 inch fat stems, and 1ft+ diameter leaves, but I'm thinking about causing one of them to pup when it really gets up in size, and has a long season ahead to get nice sized pups so I'm guessing the best time to destroy the meri-stem is probably right around May so they can be outside and have plenty of time over the summer to get nice big pups that can already be divided up by July.
I just don't feel that they are big enough to force to pup yet. In case you were interested, here's one of mine growing short and stocky.
