I do most of my work with Perl, rather than Python, but in Perl there are several kinds of stock import-level side-effects which are actually quite helpful. These are pretty light-weight though. They boil down to:
1. Global lexical changes to Perl. Sometimes this is the whole point of an import (for example Carp::Always, which typically turns any warning or exception string into a full stack dump). I can't imagine doing something like this in Python. However making soemthing like this work properly without breaking too many things requires a heck of a lot of forethought Yes, even Carp::Always may break something.
2. Manipulation of the importing module's symbol table. This is important for lexical extensions to Perl that you don't want to be global (for example Moo, Moose, and PGObject::Util::DBMethod). Among other things this allows MOPs to be added with greater sophistication than the language typically allows. I am not a Python guru but I could imagine metaprogramming side effects to be useful in setting up a consistent and powerful environment.
The problem the author describes is something which is different though, which not only is a side effect issue but also a violation of separation of concerns. There are certain problems you do not want to solve at import time, and connecting with/configuring external components is almost always one of them.
Why? Because integration with external components is almost always something you want the fine-tuning and decision-making to reside with the application developer. That's very different than setting up a consistent lexical programming environment for use (which is what the acceptable side effects do).