To give you some clues I have started using Keras for R package for deep learning.
I use an iMac with 8 GB of RAM and there doesn't seem to be a memory strain as I see from the activity log of my machine.
Any chance you would be able to provide a reproducible example? E.g. a standalone Keras script that when executed causes the associated protection issue when attempting to restart the R session?
I am seeing this as well. I have a 65MB .RData file that seems to be causing it (when rename the file before startup the message goes away). Unfortunately that file contains data that I'm using for research. Is there something I could do on my end to try & isolate the problem to avoid sharing the data?