First of all the Assassin prestige class was available right from the 3.0 get-go. It wasn't later added in 3.5, but simply modified (a better spell list, for one thing, and "sorceror" type rules for learning spells, for another).
Second, the DMG is core. It is, in fact, "Core Rulebook II". Thus the assassin was in the core books of 3rd ed. right from the get-go.
Now if you don't like the "prestige" nature of it, I assume you also don't like Bards in 1e, since they were effectively the first "prestige" class (you had to be other classes first before you could be a bard). And the bard was in the 1st ed. player's handbook but was also considered optional (heck, it was in an appendix, like where they stuck the psionics rules).
Oh, and 3rd, the 3rd ed Assassin, like the 1st ed Assassin, had a chance to instantly kill their victim. This was not the case with the Assassins in the Kit books in 2nd ed., (oddly, it did exist in a kit in the Humanoid's handbook that was not called "assassin"). So far as I know, the 4th ed paragon paths in the PHB and PHB II don't have "instakill" abilities, even if they have "assassin" in their name. Well I guess if they hit a minion it dies, but everyone has that ability.
I don't know about the Assassin class in Dragon for 4th ed. though. Does it have a chance to instakill? That would be interesting.