You could always go with a similar idea to the Holy Warrior or Champion of the Wild alternative class features in Complete Champion. Basically, in return for giving up the assassin's spellcasting, whenever access to a new spell level would be gained (perhaps a level later at 2nd/4th/6th/8th, since the assassin casts arcane spells rather than divine), you instead gain a bonus feat from a limited list. Make it so the bonus feat list contains rogue-y and assassin-y style feats and you're all set. And, since the assassin class really doesn't have a capstone ability (woo-hoo! an additional +1 on saves versus poison!), you could even toss in an additional bonus feat at 10th level for good measure.
Of course, an easier method would be to use the specialist assassin PrCs from Dragon Magazine #312 (the Oppressor, Poisoner, and Replacement Killer). Each class gives up spellcasting for a thematically appropriate set of special abilities (intimidation-, poison-, and disguise-based abilities respectively).