Yes, of course you should charge for your time - provided you make the client aware of the fact before you do so. Explain to the client that it's a free tool, but it will take x hours to set up, for which you would charge y. If the tool is particularly user-friendly, and can be set up by someone without any technical expertise, mention that fact to the client, so that she has the option of doing it herself if she wants to.
By the way, you shouldn't choose a particular tool just because it's free. Ideally, you will take a look at several alternative options, then set out the costs and benefits of each to the client so that she can make a decision. (But you can still make a recommendation.)