The licensing of the plugin should be GPL compatible. While the spirit of GPL means that the source can be modified and used in other ways, you also must properly attribute the original author. That means you can’t just make a few minor changes and claim the entire derivative work as your own. You need to make sure that attribution follows what is outlined in the license.
Keep in mind that there is a significant difference between open source and public domain (i.e. just because it’s open source does not in and of itself make a work public domain). But, GPL allows for source distribution as well as making derivative works as long as it is properly attributed.
While the general answer is probably yes, I would say that you probably should start by contacting the author first. Since what you are selling is not the plugin, but rather including this plugin with a theme that you do sell, and the author of the plugin offers a pro version, that might be a place for you to partner with them. You might look to encourage them to help you since there may be opportunity for them if users of your theme were to upgrade the plugin to their pro version.
Also, keep in mind that depending on the complexity of the plugin, you may be better off entering a relationship with the plugin author since that may make it easier for any support issues that arise.