Yes, the Disease glyph does go off spell hit. Then again, so does Icy Touch, so TBH you've got the same chances either way. Blood's rotation seems to change a little bit depending on the Death Runes you end up with because they aren't always the same, and it's also different depending on the situation. Sometimes you don't need any health back or it's an easier fight and you can use all four Death Runes to get in some extra Heart Strikes, sometimes you're taking large hits and even though they're Death Runes you're going to use them for Death Strike for the extra healing you receive in return.
TBH, I usually just work it in when I get the chance and see the diseases getting low. Sometimes I'll pop Blood Tap and use the new Death Rune to cast it and get them going again.
And Toonname, the difference isn't between just Pest/HS and IT/PS. It's between IT/PS HS/HS and Pest/HS DS, or in the case of Death Runes, Pest/HS HS/HS. Generally a DS and HS is going to be more threat for me than HS/HS and IT/PS, as well as the extra bit of healing from the DS, which is what a blood spec tank focuses on quite a bit, self healing abilities, and three HS's are going to be more than two and a couple lower damage abilities for diseases, not to mention that I take the increased crit chance on HS.
It's all personal preferrence; that's just the way I like to do it. Dark Death is also an excellent rune, but I find that one shines much more with an Unholy tanking build than a Blood spec due to the increased spell damage with Impurity.