I can't say I'm particularly surprised to see the criticism, and I certainly do acknowledge some valid points but I will say that frankly the way some PCs (or, rather, players) have reacted has been something of a disappointment for me.
(1) The honest truth is that the plague was unleashed when I was away for the day and in a way that wasn't planned for - entirely to due to the actions of Pcs behaving in an unanticipated way. The nature of plots are that they never go the way DMs plan them, and so a lot of the time we have to react on our feet and/or get super busy with things. This is both good in that we're trying to make a fluid, 24/7 world where players have a huge impact on things, and bad in that characters making certain choices can de-rail things and/or result in things happening that isn't desirable.
(2) People decided the only way to "solve" this plot would be to hack their way through everything and just kill everything, which was just foolish and totally detrimental. I don't mind it at all from an OOC perspective, but the result will unfortunately result in more hardship for the town.
(3) These sort of things do depend on any particular character, but I'd be nice for some characters (non-clerics, for instance) to remember that the canon setting of the Forgotten Realms is one in which multiple deities are acknowledged beyond a character's patron deity. Sailors praying to Umberlee to prevent storms, Beshaba at weddings, and so on. Again, characters seemed to behave in a manner that just seemed puzzling to me and a little reliant on a DM's sense of mercy to ensure that it'd "all work out" in the end.
When someone takes hostages, the first reaction generally isn't to storm the hostage takers straight away -- generally there's a period of negotiation -- in EfU, we'd describe this as roleplay. Storming the hostage-takers may well be a necessary act, but unfortunately the end result of this action by PCs so prematurely has resulted in a much longer period of the plague being so devastating.
(4) Sanctuary is awash with clerics, making this plague easily cured by a simple spell would be incredibly pointless. As it is, clerics have plenty to do by removing stat drain and tending to people's sickness as well as just RP'ing helping people. I'd find the RP opportunities in this position to be much better than a "plague" that was for most Pcs just a "very minor annoyance." There are both IC and OOC reasons for this mechanics decision.
I mean really, two clerics with maxed out remove disease could practically cure all of Sanctuary instantly on their own.
(5) The people who are uptight about the fact that a dead god is (apparently) involved... no comment.
(6) Although I agree our implementation wasn't fantastic, if you as a player feel the best thing to do is just to log off entirely and try to ignore this plague and the RP possibilities it presents, I'm really not sure this is the best server for you.
Thanks everyone for the comments, I honestly really do appreciate it and would welcome more constructive criticism throughout the course of the plot or even at the end of the plot.