If your page is dynamic, and built on the fly from parameters fed in from the URL then you should use a query string, because this helps Google to understand your site structure, and to spider and index it accordingly. Rewriting it so that it looks like directory format is a bad idea (especially if you include the parameter names within the URL). As long as the parameter values are given as words rather than arbitrary numbers/strings, this is perfectly SEO friendly.
If your pages are essentially static then it's better to reflect that in the URL structure and to avoid query URLs. Having said that, as long as you use worded parameter values you shouldn't find it has too much of an impact on your SEO.
If you have a dynamic system but with just a single parameter then it's Ok to consider it as a static structure (as we do here).
At the end of the day, what Google wants is a URL structure it can understand, spider and index consistently and reliably. It isn't interested in enforcing arbitrary rules.