I have to say, due to Takei not being in every episode of seasons one and three anyway, his slightly extended absence from season two isn't perhaps as noticable as it would be if he'd been contracted for more episodes in the first place.
The fact that they aired the episodes out of production order helped mask it too. In shooting order, he's missing for 9 consecutive episodes, and 10 out of 11 consecutive ones. In broadcast order, though, he's missing from episodes 5, 10, 13, 15-19, 21, 22, and 25. So there are five in a row without him, but otherwise his absences wouldn't have been quite as noticeable.