It sounds like you'll be safe taking the medication, but keep in mind it sounds like it was prescribed not to you, but your wife, and it's a pretty potent medication for a one-time use like you're planning, so take a low dose at least an hour or two before the flight.
Most people get valium or xanax for flight uses like this, so I don't really think klonopin is appropriate, but it depends on how long your flight is going to be because Klonopin is a very long-acting medication and can make you sedated/drowsy for several hours, especially for those (like you) who (presumably) don't have tolerance for benzodiazepine medications like the ones I've mentioned. As suggested, I would agree that 0.25mg would be an appropriate dose to take two hours before the flight. The first time I took 0.5mg of klonopin I had some tolerance from taking 0.5mg xanax for over a month previously and it relaxed me and put me to sleep for a strong 4-6 hours.
Bottom line, it's safe to take, but keep the dose really low and take it long before your flight because it's going to last a while and you want to make sure it has kicked in by the time you're on the plane and that you aren't knocked out for hours after you land :P
Good luck and be safe!