Noise evaluation can be prevented if you disable the file cache feature when you integrate a particular set of images. If the cache is enabled, noise statistics are necessary because they are part of each cache record and there are other data that depend on them.
I find it a bit annoying because MRS noise evaluation never succeeds with my DSLR images
As noted above, noise evaluation and file caching should be disabled when integrating master calibration frames. In this way no noise evaluation routine will be applied to your CFA/Bayer frames.
On the other hand it would be possible to automatically disable noise evaluation for calibration frames. This implies that we should have a reliable way to identify the type of frames that we are reading. It seems that the FITS header keyword IMAGETYP is being used for this purpose by most image acquisition applications, so I'll add this feature in the next version of the ImageIntegration tool. However, I can't see a way to identify the type of frame in DSLR images (if anybody knows one, please let me know), so disabling file cache and noise evaluation seems your only resort.