Yup, CB Activity can certainly be used as a commenting system. For Joomla articles specifically edit the "Content - CB Activity" plugin in Extensions > Plugins then under Comments tab you can enable commenting. Under Commenting and Likes you can add Joomla context exclusions as well if you don't want it outputting in certain views as well as inclusions if you want it to output in other locations.

You can turn replies on under that same tab. You've fully control over the streams parameters from there.

Under the Comments tab of "Content - CB Activity" scroll until you reach the Likes section and adjust the Include/Exclude parameters as needed. If you mean the article Likes functionality then in the "Content - CB Activity" plugin click the Likes tab and adjust Include/Exclude there. Have confirmed this works perfectly fine. In your case specifically you only need to adjust Include and set it to Like. It should automatically suppress the pop-up mouseover and just be a like/unlike button toggle.