There is absolutely no ethical issue with collecting miles on the flight you would have chosen had miles not been a factor. It's not as if you can save money, or obtain any other alternative benefit for you or them, if you forego them.

The only possible ethical issue arises if you let the potential of collecting miles influence your choice of flight or airline to their detriment. I would ask them if they have any travel policies you should conform to, anyone you should use to book your flights through, or anything else you should know before booking. This is a reasonable business question. It can only improve their opinion of you as someone who understands this stuff.

Then, be guided by their answer. If you must use a certain agency, tell them what airline you'd prefer to use. They'll use it if the fares are the same, and probably if they're close. Otherwise, they won't. If there's a policy, do what you can within its constraints.

Once the flight is booked, if it's not on your preferred airline, join its FFP or that of a partner on which you can earn miles for the flight. At least you won't lose all credit. If you take the job and end up on that airline a lot, you'll be off to a good start!