(Having not actually heard much of the commentary that followed that debacle . . .)
The context of a place-kick played a major part in the penalty, and could explain Joe Gibbs' confusion.
Many people know that consecutive timeouts are not allowed. However, in most cases, officials simply choose to ignore the requests for a second timeout and the play continues.
Somewhat recently, I'm led to believe, this rule was amended to state that in a play in which a kicker is involved, and the request for a second timeout is used to freeze or distract a kicker, then there is an unsportsmanlike penalty.
I'm trying to find a source to back this up, but I've been told that it is now considered unsportsmanlike conduct because teams (specifically the Patriots, originally) began taking advantage of the rule by signaling for a second timeout knowing full well that it would not be awarded, but just trying to distract the kicker.
As the intent of this signal was not part of the normal course of the game, but instead was specifically meant to be a coercive use of a rules loophole, the rule was changed accordingly.
This is why Tony Corrente specifically noted in his on-field call that the second timeout call "meant to freeze the kicker", was a violation and a penalty by rule.
So, I find it understandable - inexcusable, but understandable - that Joe Gibbs may not have been fully clear on the rule. My feeling is that he DID know the rule and was covering for himself or a player, but there's some plausible deniability there.