Your idea about a standard case fan is actually a good one. Arctic Cooling makes some really quiet ones that are not expensive. There are plenty you can get for under $10 (US). Those are the only case fans I use in my own builds. I usually pick them up from Newegg. Not sure where you are in the world or where you can shop, though.
A fan controller is also a decent investment. You can always move it to another machine in the future. I know this does not address the original issue of slow-turning fans, but it is an inexpensive workaround/enhancement.
On the Dell hardware I run (Dimension B110), I can actually hear the exhaust fan gradually spin up - especially during heavy flash/Java use or the MintUpdate I performed this morning. Eventually, it will gradually spin back down. This tells me that the Dell and Mint combo does indeed control the fan speed and cool down what is necessary. Sadly, GKrellM does not display the temps on any of the Dell hardware I have used, or I could give you some specifics.
None of my machines dual-boot or have any Windows software installed. They only run one OS. The ones running Mint have no problems with fan speed, so I am thinking it must be something not functioning as good as you need it with your motherboard/BIOS. Good luck, and please keep us updated as to how you get everything worked out.