It seems like the noise might not be due to enfuse.
If I merge CR2 in Picturenaut directly the exr output has a strange color cast in gradients, but merging otherwise smooth tiff files results in severe noise in the hdr.
The left image is made of tiffs from darktable/rawtherapee, the right one is using original CR2 files.
I'm currently trying to do everythingin hugin, but that usuallyfails. It might be due to highlight reconstruction in rawtherapee, but darktable results with the same issue.
Is this the same issue you (or others) solved with colorspace flag?