The only way I could see of bringing back Stephen in any credible way, would be through another timeline in which he is alive through a differently evolved world but is still the same person. The next best thing is that he is a completely different person, but not terribly different (Claudia/Jenny). But it would be pushing it to make him part of the ARC, like they did with Claudia, which I thought was a bit far-fetched.
The problem is that anomalies behave erratically - they appear, disappear - or never completely disappear. We know they move and open up into different prehistoric eras and now the future. Now we know that there are anomalies within anomalies! (Remember the 'spaghetti junction of anomalies' in the dodo episode?). Then there are the differing timelines!
I am reminded of the conversation between Nick and Stephen in the raptors episode, where Stephen says to Nick that he could change a million things and still not get Claudia back.
And say Helen did resort to cloning: it would not be the same Stephen in terms of personality and character, even though physically identical. It does seem impossible to have produced those clones of the 'cleaner' for them to do the same job as the original man: did she clone his personality and identity too? It seems illogical: she would have to know what the original man's upbringing was like and to re-enact it, and we know that that is impossible. I would be interested to know how she managed it. Maybe she found him alive in a particular timeline. But why go to so much trouble for this selfish, obscure and annoying man who she barely knows? Are all things possible in sci-fi, or do events have to be grounded in some kind of reality that makes sense?
As an aside, frankly that man would be the last person I would want to clone. Just goes to show, Helen is not a good judge of character: