I'm not a architecture photographer, but I do live in Ghent. I don't think setting up a tripod in certain Churches will be a problem, since you will probably have to pay for entry. Sint-Baafs churche will probably be the most impressive, but also attracts most tourist, so I don't know how easy it will be to take photographs without beeing disturbed to much.
You should certainly visit the old part of Gent near the "Graslei", "Korenlei" and the castle "Gravensteen". I think this is the most beautiful part of Ghent, especially by night, when you get reflections of the buildings and their lights in the water.
If you want some more information don't hesitate to contact me.