My brother has this exact problem. Up here in Canada we have one discount airline called JetsGo and the Air Canada discount version called Tango. His company wanted him to take JetsGo to save $40. He refused (quite boldly I might say)saying they only fly a couple of times a day from YYZ-YUL. Tango can link to Air Canada's hourly flights if there are any problems as they are the same company.

Turns out a HUGE snow storm blew in and my brother was on Tango and was put on an Air Canada flight 5 hours later. The JetsGo flight didn't even get into YUL. Look at the cost of just 2 taxis (hotel and back), 1 hotel and meals. They just blew a whole other ticket with that plus lost work time.

Also, try to explain to your boss about productivity. Try to figure out how much you make per hour and then ask your boss if he prefers to see a savings of $40 on airfare or the lost cost of you working. I don't care what anyone says, you can't get meaningful work done in economy if the middle seat is full.

Anyone in sales can prove that the lowest cost is not always the best option (sometimes it is-but not likely here). Its about value. Waking up at 4:00am isn't going to allow you to give your boss a true days work when you are that tired hence bad value for the company when it tries to save money off bad routings.

I would almost beg your boss to have her go on a few of these trips AND then make her do her regular job as well and see if she thinks $20,$40 or even $100 is worth the savings.

Best of luck and let us know how it turns out.