Kyle,
I don't believe four nights in Bayeux will be "too much". As you're taking a two-day BattleBus tour, you'll need three days at least (arrival day, Tour Day 1, Tour Day 2 and free day).
Rather than take the time and effort to change Hotels for one night in Honfleur (or other location), I'd suggest using the time to:
explore the wonderful small town of Bayeux (there are some nice restaurants there!)
perhaps take a day trip to the Museum in Caen (one of the best, although you could stop there for a few hours on your arrival day also).
explore the WW-II Museum in Bayeux.
if you have a car, have a look at the Gun Batteries at Longues sur Mer, provided those aren't covered on the tours you'll be taking - the Batteries are only about 15 minutes outside Bayeux, and you'll probably recognize them from The Longest Day. You can rent a car for the day if necessary - ask your Hotel to make the arrangements, especially if you don't speak French.
visit the historic Bayeux Tapestry, which describes a much earlier battle.
After two full days of tours, I feel there's more than enough to keep busy with around Bayeux.
Happy travels!