Okay I'm having to type is again, because this crappy website timed out so I'll make it short:
1. Apples to apples comparison, with time MCEBuddy profiles have gotten better in quality and faster in speed. I.e. MP4 High Quality has gotten better in quality and needs more time to convert, where as MP4 Fast has becomes faster keeping the same quality or better.
So really you need to evaluate what profile you're using, it's High Quality, do you really need the quality or speed of Fast? Maybe try Normal as a compromise.
2. This is a very CPU intensive process with CPU running anywhere between 70 to 100% depending upon the number of simultaneous conversions. Having said that the CPU fan noise depends on your system configureation. Remember, faster CPU's, more RAM , more Cores mean MORE heat and it means higher fan speeds to keep it cool. Also design plays a huge role. My E6410 Dual Core runs a heck of a lot more silently than my M6400 Dual Core. So I use an external fan with my M6400 which is much more silent and keep it running cooler and at lower internal fan speeds. (Commercial skipping is even keep on CPU Util, it's recoding that takes CPU and those too are profile dependent - e.g. Divx profiles are VERY CPU intensive compared to MP4).
Try what I do at night on my workstation, I set the priority to low which generally keeps it running cooler and more silently.
To recap:
1. Check what profiles you're using, there's a trade off between quality and speed, apples to apples, new profiles/versions are faster and better in quality
2. Use computers with lower heat specs /external and low priority to keep it running cooler and more silently.