It isn't that Pat was insufficiently sexy, it's that she had other obligations. Remember, most pilots fail, and B5 wasn't picked up until more than a year after the Gathering was filmed. She didn't have a contractual guarantee so she took other work and wasn't able to come back for the first season or most of the second. Incidentally, she just gave birth six weeks before this episode was filmed.
JMS made it clear in the script books and Pat expanded on it in her book (Pleasure Thresholds) that the studio flat out didn't want her for a number of reasons (more stunt than acting credits, and possibly bad feelings from an exec who tried to casting couch her) and ensured it by a too-low contract offer. When she passed on the offer, JMS was away and couldn't try to re-open negotiations.