How to make a read protection on eMMC?
Do you mean read-only?
Or do you want really that nobody is able to read from it? Then just remove the eMMC module or don’t mount it?
I want really that nobody is able to read from eMMC
what is stored on the eMMC?
I assume that the read-protected status shall only be timely limited, i.e. a kind of “storing information and prevent others reading it” (e.g. after a system startup procedure with read access).
<joke>
Otherwise:
A long time ago, in a Chip magazine at April 1st, there was an article about a radical new memory type:
WOM → Write only memory. 
If the state shall never be set back, a simple chmod -R 000 /mnt/<diskname> resp. chmod -R ugo-rwx /mnt/<diskname> could do the trick. Never tried this.
Another option could be rm -Rf /mnt/<diskname>.
</joke>
Still, I like to understand the use case. What is the eMMC used for? To host some confidential data or is it the whole operating system? At the end it sounds like disk encryption. Which is going to work for a data store but for whole os, it will be challanging.