I read that it was fine to use the free one because it has less features and ads. If you pay the fee you can disable the ads and use the extra features. I don't think it's anything to worry about. If your site is big enough for Google to notice and ask you to take down your google maps integration, you have a good problem.
Use of the regular free Google Maps API is not allowed for sites that aren't available to the public free of charge.
"The Maps API is a free beta service, available for any web site that is free to consumers. Please see the terms of use for more information" (from: http://www.google.com/apis/maps/ )