1. Can take travel domain... but do they?
If their god offers it, absolutely. The domain power and spells are all fantastic.
2. Fly can be cast on allies, party wizard casts fly on party fighter to have him grapple BBEG wizard
Fly is a 3rd-level spell, which you're not going to have EVER against a 3rd-level BBEG Wizard.
3. Non core, but if your DM allows it then sure. You did waste a round escaping from the grapple after discharging it (unless you discharge it preemptively)
It's from Complete Mage, so "if your DM allows it" is realistically "any game that goes outside core at all."
4. Dispel, counterspell, and dimensional anchor
A dedicated Cleric dispeller can, indeed, be a powerful force. You will have to beware, however, of Spellblade weapons throwing those Dispel Magic attempts right back in your face. Counterspelling is a fail tactic because of feat taxes until absurdly high levels, failure state in that you're almost certainly using Dispel Magic to counter, and at absurdly high levels the name of the game is contingencies. Finally, Dimensional Anchor just might be the worst spell in the game. It has two failure conditions (ranged touch attack, which many spellcasters can just plain immunize themselves against, and Will Negates saving throw, which ALL spellcasters have in spades) and locks down the use of the least offensive subschool of magic. Even if you land it, your spellcaster just spent a turn blabbering while the BBEG can now say "Oh, you don't want me to escape? Ok, I'll just murder all of you, then."
Also, congrats, your BBEG managed to counter a level 1 spell and a turn of the fighter by using up his entire turn AND a high level spell. Party still ahead on the action economy & resources (spells). AND the methods given to counter this are only available for fullcaster BBEGs. 
This means that what I proposed is indeed an effective strategy. It is just not an unstoppable "I win you lose". And note that I didn't propose it as the IDEAL strategy, I proposed it as a counter to "this spell is worthless"
You can't seem to decide whether the BBEG is a Wizard or has grapple mods significantly superior to the Fighter's. Not that it matters all that much, because past level 7 they can both be true, anyway. In any case, you're also conveniently ignoring that grappling has no less than 3 failure conditions to start a grapple with an unwilling opponent. First, the opponent gets an AoO and the attempt fails if said AoO does damage. Second, you need to succeed on a melee touch attack, which becomes progressively easier only as blanket immunity to grappling becomes more prevalent. Third, you need to succeed a grapple check to actually grab the character. This isn't even counting the hidden fourth failure condition that you need to get into melee in the first place to start a grapple. Your suggested methods to get around this? The Wizard casts Fly on the Fighter so the Fighter can hover over to the Wizard and hope to grapple him before the Wizard throws down a horribly debilitating AoE save-or-lose like Stinking Cloud or Black Tentacles.
In any case, how do you know that the party is fighting the BBEG at full strength, anyway? Let's say the party is 5th-level, and they're trying to deal with a 7th-level Necromancer BBEG. I'm willing to bet I could set up a dungeon that would render the party virtually incapable of even getting to the BBEG through simple application of the BBEG's spells. Making it that unfair for the party is probably not even all that hard.
