"I've found an application note how pins and gpios are to be used. There is an example how to make/break connection to analog globals(in order to switch analog/digital input which shares same GPIO). Is it practicable to do so in my case?"
My assumption has been wrong, as multiplexer component does exactly the same thing, doesn't it?
Does it make sense to change drive mode to internal pull up in order to make inputs more resistent regarding emc?