It seems that especially early on rebellions are actually quite a good thing - especially if the rebels are the earls of some minor county. I was playing the Duke of Toulouse and only started with two demesne. Then two earls rebelled because they wanted me to adopt that elective assembly thingy. Needless to say they were crushed, imprisoned and had their titles revoked. You can also go the whole nine yards and have them banished for a substantial gain in money if you don't mind the relation hit. I pretty much doubled my land and my income after taking their counties.
Also another thing I noticed was that sometimes you want your imprisonment to fail. Say for example you uncover some dirt on one of your earls. If you successfully imprison them than that's it. You can't revoke their titles without taking a substantial penalty hit in your relations. But if you fail to imprison and they rise up in rebellion, than you can quite happily crush them, revoke their titles without any penalties and carry on expanding your demesne. So maybe there is an argument for not having a super high intrigue rating.
Also another thing I noticed was that sometimes you want your imprisonment to fail. Say for example you uncover some dirt on one of your earls. If you successfully imprison them than that's it. You can't revoke their titles without taking a substantial penalty hit in your relations. But if you fail to imprison and they rise up in rebellion, than you can quite happily crush them, revoke their titles without any penalties and carry on expanding your demesne. So maybe there is an argument for not having a super high intrigue rating.