This has been a long-running item of concern since day one - and it basically boiled down to installing the running boards which were an option initially. In Canada, they installed them under a warranty item for those that had that issue with the paint. Those in the USA were not so lucky with the warranty if I remember right. But you say running boards are not an option for you - but they are the best "fix" - so..............
A lot of people also added mud flaps to the front that seemed to help, but they are not a total solution that is for sure. It's the design of the car that results in those fender chips, and is not different from a lot of other cars, that have the same issue, and the car is 6-7 years old - it isn't a spring chicken anymore.
A good alternative to the running boards is that clear plastic armour that is also used for invisible bra's to protect the paint on the front of the hood, fenders, and painted bumpers. Check your local body shop or a place that does window tinting etc. - they should be able to help you out with that.
Here is a place in Middleton:
Re: the seams on the doors - you might also want to get some rust proofing down on the inside of the door seams.