Yes, the fiancée visa is multi entry. But I think there is possibly a misunderstanding; you don't apply for further leave to remain AFTER six months, you need to apply WITHIN six months. I wouldn't leave it to the last minute.
But no, they shouldn't bother you about going on a honeymoon and returning whilst still on a fiancée visa.
It may be a good idea, to dispel any doubt, to have some evidence of applying for FLR(M) on your return, such as tenancy agreement/mortgage statement, and sponsor's payslips or employment letter (or any relevant evidence if you are meeting the requirement in some other way, such as savings or self-employment).
Oh, I thought I had to wait til 90 days of my fiancé visa expiring to apply for the next visa which would give me the 2.5 years? I can apply whenever after I'm married? Thanks for answering the honeymoon question.