My partner and I had a canasta of 9s and I had a pickup which contained three 9s which I held in my hand to use as fairly safe discards because the pack was frozen. I used one of them and then my opponent threw a 9. Could I pick up the pile with the pair of 9s I had in my hand?
Yes, you can do that. From the rules:
UNFREEZING THE DISCARD PILE
A frozen discard pile is unfrozen only by being taken. When the discard pile is topped by a wild card or a black three, at least one natural card must be discarded on top of the pile before the pile may be taken. Then, a player may take that card (and the pile) only with a natural pair of the same rank from his hand. Before touching the discard pile, the player should show the pair (together with any additional cards if needed to meet the minimum count of an initial meld).
As long as you have a natural pair in your hand, it doesn't matter what else you have on the table. In fact, it is a common strategy to not add to an existing meld (even if it would form a Canasta!) to make your opponent think that a particular rank is a safe discard on a frozen pile.