I agree with you that cleaning only part of the print would be quite incredible, no matter who would be the cleaner.
But I cannot agree that it MUST have been cleaned up. There are various other possibilities. More probable possibilities. It's quite possible the bathmat didn't remain in the same position after Guede left the mark. As it was quite diluted and quite incomplete, it is questionable if the police recognized such a diluted stain as part of the bathmat mark. If they found it at all, as they shown they miss some more obvious prints, like the ones on the pillow. Moreover, many people went through that bathroom before any collection of evidence commenced - it could have contributed to the stain being not recognizable.
Such a scenario rings more true to me, than a scenario when someone purposefully cleans up only part of the print and leaves the rest.
As you see, this is not the way you can exclude Guede as a source of that mark.
BTW I think the bathmat was collected before any tests for residual blood were made in the bathroom. So the connection of any stain with the partial print would be even harder to made. I recall the photo of the "pink" bathroom and a comment that they botched that test, so no meaningful results were achieved. If the diluted stain was not visible, they lost the chance to discover it.
