Andy, I'm sure Carol will be right and sorry if I misled you (maybe regs have changed; maybe it was a senior moment). Despite age and memory loss, I know
that I've read somewhere that the company is animal friendly. If not allowing dogs into cabins I'm pretty sure they have kennels and allow owners to walk their pets.
You could always try the horse's mouth. Anek have what looks like a shiny new web site and a page full of contact info, including e-mail, so it might be worth asking exactly what they offer.
We've never sailed with Minoan so can't comment but we've been several times with ANEK and have always found the boats clean, comfortable and with excellent facilities (except one trip back from Pireas on what I think was the oldest, smallest boat in the fleet. Getting on/off the car deck was like driving on a narrow spiral staircase).
On a more general note I've found the michelin website very helpful in route planning for travel across Europe.
If you click Show/hide stopovers you can enter chosen intermediate places if you want to go somewhere particular and under route type there are various choices - recommended, shortest etc. and various other options - avoiding tolls etc.
If you request the complete route first you can then break it down into shorter sections (as short as a few miles/kms if you wish) and vary the route as much as you like. You can also print out detailed directions with distances/estimated times/costs etc and they're even pretty good detailing any current roadworks.
Enjoy the trip.
P.S. I'm NOT an agent for ANEK.