The best way to avoid the research choice pop up is to pre-plan your tech research via the tech tree. Open the Science Advisor, click and shift click until you get an order of research you like, then when you finish one tech, you will quietly proceed with the next one.
This is not recommended for long plans, as the world situation constantly changes and you should be flexible in your research to adapt. However, you can always go back into the science advisor and re-arrange things. No beakers get lost for techs you have partially researched.
Don't considier it an annoying reccomendation. Just consider it insurance against spending turns researching nothing at all. Because the only time this pop up happens is when the game does not know what you want to do next, so it asks.