They'll probably have to let her go. Either killing her off or maybe write her off the show by another means.
The idea they could write her pregnancy into the show is unlikely. For one, her character was never seen interacting or even caring about Bob (or vice-versa) until they were forced together on the road after the prison fell. That was the time they started to bond. But that situation would not give them any opportunity to have a roll in the hay. They were in tight spots all the time, They certainly weren't having relationships in the boxcar, and they wouldn't have had any time alone after the escape from Terminus. So saying she got pregnant thanks to Bob would be a stretch.
Plus, even though the show has been on for 4-5 years now, only about a year or 2 has gone by in the story. The time between episodes and sometimes tv seasons are usually just a few days or a few hours. They'd need a several month timeskip if they were going to say Sasha got pregnant and why she's got a baby bump already. And I don't think the current flow of the story would allow for a time skip like that. But I guess we'll find out where things will leave off at the end of this season.
Also, I would tend to consider an in-show pregnancy as a death sentence, anyway.
If they don't start shooting the next season until after the winter months are over, she'll definitely be showing that baby bump. Even if they used a lot of clever camera angling, doing a lot of fighting/action scenes, being on your feet on set, and daily activity would be asking a bit much of a pregnant woman. It's not like they are in the prison anymore. I suppose they could find Sasha a poncho to wear, but it's still stretching things a bit on an action show like TWD. She'd need to disappear eventually for several months after the birth to nurse and care for the baby and herself (as well as lose any baby weight to maintain consistency) before she could think about returning to work. She'd be giving birth right in the middle of the months where they do their filming.
How they could write her off... I don't know. A sudden death at the beginning of season 6 would be pretty lame. But probably necessary if there isn't a place they could realistically leave Sasha behind or explain why she'd suddenly want to leave the group. I can't see a gentle and loving character like Tyreese's leaving her behind all alone, though. Right now killing her off suddenly in the first couple of episodes of season 6 seems about all they can do to explain her removal of the show without breaking up the cast or disturbing the current storylines flow.
The only thing that would work out for her character is if the show reaches the Alexandria Safe-Zone from the comic book by the end of season 5 and she blends in with the rest of the people there and rarely appears through season 6 of the tv show. But she might be killed off there anyway.