I recall reading somewhere that the character was sidelined for awhile so the writers could figure out what to so with her. Though my memories of the show doesn't seem to back that up.
You are correct. Troi/Sirtis is missing for several Season One episodes, although contractually she was paid for them. The producers were close to writing her out, but the departure of Denise Crosby - and then Gates McFadden - saved her. They didn't want to start Season Two with all three female cast members missing.
So they decided to build Troi an office set, so she could counsel patients away from the bridge, and also decided on a bar set (Ten Forward), where counseling also might happen. However, Whoopi Goldberg's several requests to join the show were suddenly believed by those on high - and, as progress had already been made on a bar set, Guinan became the character who did the counseling from that set.
Sadly for Marina Sirtis, every time Whoopi indicated she was free to film a new episode, it was usually a strong Troi scene that was hastily rewritten for Guinan. And they didn't really get around to building the long-promised office set for quite some time.