There aren't many prestige classes I like, but the overall concept doesn't bother me, and some of them are quite cool. I've got no grudge with the assassin class. I think that people who are outraged over the spell-use are just touchy about the over-all prevelence of spell use, more-so than there being anything inherently outrageous about a magic assassin. (Which, I agree, gelds well with the dmg description, which makes it clear that it isn't a generic "kill-for-hire" class)
As for the issue of giving classes and prcs spells in general...I understand how it seems lazy and lame, but it's really done because it's so convenient to fall back on the existing rules for mystical abilities--The assassin spell list, for instance, is small, focused, and flavorfull, taking a subset of spells from multiple class list (and shuffling spell levels in some cases) to give each assassin access to a pool of assorted mystical abilities potentially useful to a determined and subtle killer. I mean, you can give a prc a quasi-invisibility special ability, or you can just reference the invisibility spell. Same for other appropriate abilities already well covered by phb spells.
I see giving prcs these sort of limited, unique, spell lists (rather than actual caster level advancement) as shorthand for "mysterious mysticism/magic utilized by this class" as opposed to representing formal training as a priest or wizard. Just because they utilize existing spell and spellcasting mechanics doesn't mean the flavor can't be anything you want, especially when you're talking about a limited pool of powers and a caster level that doesn't stack with any other class.
Granted, just making a class who gets a handful of spells is incredibly lame, but I haven't noticed limited spell-casting used that way. Spellcasting isn't the defining feature of the Assasin prc, for example, it's just a way of rounding out it's abilities. (And expanding them even, through the addition of assassin specific spells in some splatbooks)
