Partly because Michael O'Hare needed to be swapped out at the end of season 1, but also partly because what ended up being the story of seasons 1-4 was supposed to be spread out over an entire franchise of series with two 5-year arcs each.

JMS supposedly had contingency plans for losing any of the actors, but O'Hare in particular was difficult because his character was supposed to be the central mythic figure. (This is why he shows up again later on as a guest star; one specific aspect of the character was already set up to the point that they couldn't work their way out of it easily.) Unfortunately, O'Hare had to leave the show for health reasons after the first season.