The concern is absurd. The rule applies to acceptance of gifts only if that gift is not available to everyone. If Staples offers a free binder in a back-to-school sale, government employees are free to accept it, because everyone can. Furthermore, I think the rule applies only to personal gifts; items offered for government use are not covered. And of course, as the previous comment points out, the full price (nothing) has been paid.
All agencies should have either an ethics office or a legal office that would clarify this with a phone call. So it's pretty clear that this is a red herring; the people who brought it up won't adopt free software for some other reason, not for the stated reason.