Is doing a research internship during MSc. studies worth exceeding the standard period of study?
This is a matter of balancing trade-offs and can be viewed in a variety of ways. While I won't go into all of the many ways, here are two ways that taking the internship could be perceived: 

1) You were not able to commit to something you agreed to commit to at the start. Your leaving for a better opportunity may be interpreted by potential PhD supervisors as an inability to stick with a program. 

2) You found an opportunity to build a new network of collaborators, gain new knowledge, experience, and perspective. You will also be making money, which can be used to make your life easier later on. 

There are infinite ways to view the trade-offs, but only you can make that distinction.