I've had experience of this. It's good to make clear to the client that you've been hired for a specific purpose and that you can't perform your contracted job properly if a third party won't comply with your instructions.
It's in the client's (and designer's) interest to listen to you. Your reputation depends on your advice or consultation proving successful and if they're aware of that it should help you.
If you have a particularly awkward client who is keen on some useless keywords then it's kind of your job to tell them so (but in the nicest possible way). Compromising and giving them half of what they want, coupled with your own input, can help them move away from their own ideas when they eventually realise that your advice is paying off more than their own thoughts.
Partial SEO can be worthwhile. If by this you mean just on-site SEO then it can go some way, but if there are few valuable links then it's not going to stick around at the top of the SERPs for too long. If it's just on part of the website then it might be worth doing so long as the client is aware that further work should be undertaken later on to make the most of the opportunity.