That doesn't make them bad. It's hard to call Deetsan or Kud-ei bad people, even when they don't follow the rules to the letter, and the worst you could say about Adrienne Berene or Agata was carelessness, seldom a mortal sin. Some, like S'Drassa, look wasteful (skooma and an obsession with crystals) until you hear the full story (trying to find a cure for addiction, and the crystals are said to have healing powers). Wasteful comes to mind, but we're talking a group that's had no reason not to waste time for centuries.
And there are plainly evil individuals. Deetsan's former guild leader is the most obvious of this, but he's not alone even in Oblivion, nevermind Morrowind or Daggerfall. Does a single murderer corrupt the souls of a thousand other men or mer? While Jeanne Frasoric is no doubt a literal example of Peter's Law, she's also trying to be better, and her political and social connections could well be worth the figurehead. Does her lack of skill weigh on the abilities and minds of a dozen others? They kill the dangerous and those that could be dangerous, but at some point the question arises as to how far pacifism must be pushed.
At least in the Elder Scrolls universe, corpses given last rights can not, by the nature of Arkay, be used in necromantic rituals. It's a mutable law -- Arkay's Blessing is supposed to keep you from soul-trapping people, but Mannimarco wrote a loophole into it -- but it's a fairly effective one. Individuals who want to prevent from becoming undead can do so, if they die someplace that they'll get Arkay's ritual after death. See http://www.imperial-library.info/mwbooks/corpse_preparation.shtml for a reasonably educated source. Cannibalism, cremation, or significantly accelerated rot can all make corpses non-viable for Necromancy, as well, although significant effort must go into it, as the ashpits of Morrowind are not enough. The world of Nirn is a dangerous place, so this is a reasonable and major concern.
But a lot of people aren't subjected to those rights, either because they died without a nearby religious available, or due to the interaction of the Necromancer himself or herself, or because they did not ask for such. The second attribute is of significant concern, as the most valuable necromantic rituals (especially related to lichdom and life extension) involve quite a few corpses. The aforementioned loophole regarding Arkay's Blessing is of greater concern, as it provides a way to trap the souls of the living and only operates through murder or death.
That's not to say that a "good" necromancer is impossible within the setting's definition, per say, although we see few or no such beings in Oblivion (and it may be a practical near-impossibility due to the definition of Necromancy used by the Mage's Guild, which defines Necromancy as only mentally damaging and unsafe spells). But it makes concern about them problematic,