I Agree with you to a point....
But like I posted earlier it depends on the mileage that you are doing... If it's only 5K a year then a diesel cost more overall if you do 50K then a diesel will save you bags of money...
Hence why I said do the sums...
and are cheaper to fix when something goes wrong!!
What a diesel may cost for more serious repairs it more than makes up for in economies of scale re mpg and cost per mile.
Milage is not an consideration, as it's usage dependent. Using milage as a basis as per your reasoning, the only reason I can see a petrol winning over a diesel is when it is shorter stop start journeys and inner city driving (in which your point is completely valid). However, even then the only way a petrol benefits is when it is a tiny engine pisspot i.e. aygo or similar.
Looking hypothetically:
5k miles a year, of which lets say 50% is motorway, (now with current mpg ratings you could go down as low as 30% of motorway usage) and the diesel is still going to be more cost effective to run, to the point of breaking even with a similar petrol.
I can understand your point completely, but the op is after something to benefit him long term from what I have read, and the diesel will tick all of the boxes, with little compromise. BUT if he can afford it, keep the petrol for some fun and back road blasts, as a free revving engine is always a good crack.
I have done my sums by the way fella, I work in a tier 1 OEM diesel supplier as an applications engineer, so this is kinda my job.

I do however have all the time in the world to discuss things like this.