You have to pay for vSphere with its various modules and extra features but not to use the vSphere Client to connect to a free ESXi.
I think where you may be getting the license message from is although ESXi is free, you still need to request a free license key from VMWare.
Login to your ESXi box with vSphere Client and go to Configuration -> Licensed Features -> Edit.
If you are set to evaluation mode, that is what you are getting the license warning from.
VMWare should have emailed you a license key when you signed up on their website to download ESXi. If not, you can go through the download steps again and the license key should be on one of the pages.
For me, if I go to https://www.vmware.com/products/esxi/ hit Download, login with my free VMWare account, then on the page with all of the download links, at the top of the list is my ESXi License.
The reason you are seeing the license message about vSphere is that in the Evaluation mode, some of the extra features that are only available with vSphere are enabled, once you enter a free ESXi license, those will be disabled and you won't get prompted anymore.
Also, you can use the vCenter Converter in the standalone mode (runs off of your workstation) for free with ESXi. This tool is immensely useful for moving VMs on and off of ESXi. http://www.vmware.com/products/converter/.
Personally I don't see host profiles as being that big a factor for you. You're dealing with a single host with no licensed features (DRS, HA, etc). My opinion is that it's probably easier and faster to backup your VM's, rebuild the host, and restore your VM's.
This product simplifies the task of backing up and restoring your VM's and does it relatively quickly:
http://www.trilead.com/
Best Answer
Did you try to revert to evaluation mode, enable remote SSH tech support and then back to your free license?
Using the evaluation mode is great, it allows you to use some of the enterprise features for up to 60 (completely individual) days! :)