Defeating enemies with doom tokens on them is an intended manner of managing the game's current doom total. Kill 'em all! Unless total doom's going to tick the Agenda over regardless, in which case, eh. Maybe kill 'em. If you like.
Edit: oh and the relevant rule text is Rules Ref page 14, Leaves Play --
The phrase “leaves play” refers to any time a card makes
a transition from an in-play state to an out-of-play state
(see “In Play and Out of Play” on page 13).
If a card leaves play, the following consequences occur
simultaneously with the card leaving play:
* All tokens on the card are returned to the token pool.
* All attachments on the card are discarded.
* All lasting effects and/or delayed effects affecting
the card while it was in play expire for that card.