I have finally solved my issues with El Capitan Mail app and (in my case) Exchange Servers.
This is what I have discovered;
The problem:
Mail app at El Capitan create massive debug logs at ~/Library/Containers/com.apple.mail/Data/Library/Logs/Mail/
The debug log it's not running all the time, only sometimes start a crazy loop, that you can't stop anyway, it's doesn't matter if you close the app, because it will continue next time you open Mail.
When the issue it's happening the Mail app processor use it's over 100% and the file XXX_IMAPSyncActivity.log starts to grow up to the infinite.
When the file it's too big, Mail tries to archive and zip the file, and this eats all your ram memory.
At this time you computer it's completely lost, and your only option it's to force kill Mail app or a hard reset.
If you open Mail again the process will remain at the last point and you will lose your computer again.
At this time you can remove all log and zip files at ~/Library/Containers/com.apple.mail/Data/Library/Logs/Mail/ restarting the process from the beginning.
It doesn't matter if you activate, deactivate, delete, reconfigure, rebuild or whatever you want to do with the conflictive account.
it doesn't matter if you do a clean install of El Capitan and start from zero.
Soon or later the log will eat all your resources, your processor, your disk and your ram and you will lost your computer control again.
My solution:
Probably you need to uncheck first:
Mail --> preferences --> accounts --> Mailbox Behaviors --> Move deleted messages to the Trash mailbox
And after that, disable:
Mail --> preferences --> accounts --> Advanced --> Compact mailboxes automatically
I have seen that when Mail tries to compact the mailbox with Exchange Servers the process doesn't work as expected and loops an indefinitely error.
The debug and log of this error it's what in my case created all my problems with Mail.
Disabling the automatic compact mailbox for my exchange account I have had no more issues with the Mail app at El Capitan.
I hope this help others with the same problem, and Apple programmers to definitelly solve the problem in a next update.