I personally feel like they shouldn't get their cutie marks during MLP:FiM. Their sole purposes in the show is for them to be constantly looking for their special talents (even though it's set out right in front of them) and never truly finding them. When FiM's time comes to a close, though, I think it would be a good pickup to have a bit of a time jump -- the CMC being approximately the ages of the current Mane 6, and already having their cutie marks. That way, you can continue on the idea of what's going on, but also have a fallback episode if writer's block takes place. Said fallback episode would explain how/when they got their cutie marks.
This, of course, is just my bitcoin. I refuse to read any "official" things about any of the characters in assumption that there will be a spoiler in them.