The problem with auto boxes is just as common with petrols as it is with diesels. AFAIK, the torque output of the diesel engine is not the issue.
The problem is the stupid 'sealed for life oil' policy; don't believe it! Metal contaminants buildup, filters eventually clog up & the oil will breakdown at some point too.
To be safe, change the oil & oil filter every 60k miles, also you don't need to use BMW's own oil, which is a total rip-off (£20/ltr if you can get them to sell it to you!). VW/Audi/Seat do EXACTLY the same oil for 1/2 the price, & you can get it in 1 ltr bottles.
For proof that the oil is the same, checkout my post here http://www.bimmerfest.com/forums/showpost.php?p=5253079&postcount=189 with links to the gearbox manufacturer's site.
BMWs manual transmissions are not very reliable. I had a 2006 320d M Sport that needed a gearbox replacement under warranty at 28,000 miles, plus it also suffered two dual mass flywheel failures. By chance, I bumped into a BMW technician at a party a few months ago, and got chatting. He told me that his dealership sees two or three diesel manual 3 and 5 series a week with transmission problems, often with as little as 20,000 miles on the clock. It is a well known issue. He reckons the autos are more reliable.
My last two cars (both VWs) have had dual mass flywheels and manual transmissions, and both did over 100,000 miles without a problem. I didn't drive the BMW any differently to the Volkswagens.
Just because you had a freak failure at 28k, doesn't mean all BMW manual gear boxes are unreliable! LOL, you gotta look at the bigger picture, not just your car.
Your gear box may have failed due to the faulty DMF; odd that you had 2 fail though at such low mileage...
My 330d manual has done 103k, & so far the gear box & DMF are OK.
I question whether that guy you spoke to really was a BMW tech, I'll have to ask the one I know.
Anyway, I highly doubt that manuals are less reliable than autos; manuals are much simpler in build, so less to go wrong. Google 'bmw box failed/died' etc & you will find that amongst the 1st hand reports they are largely BMs with auto boxes!
My 2006 320d manual had two dual mass flywheel replacements, and one complete transmission replacement in 2 years / 42,000 miles.
Like the previous commenter, I have racked up several hundred thousand miles in other DMF equipped diesels without a single incident.
My brother in law is a BMW technician of 10 years experience, and reckons that the reliability of most BMWs from around 2005 onwards is nowhere near their historic level.