While I don't think we're going to see the end of Marten and Claire's relationship in this storyline.
What we are seeing is the end of the cutesy-lovey-dovey stage of their relationship and we're moving to a point where they're starting to notice the other's flaws.
In Claire's case, its realising that her boyfriend has no real plans for his life and that its a long way before he's an adult.
In Marten's case, its realising that Claire has a little too much of a control streak in her and is more than a little ruthless.
This storyline could be setting the stage for future plots involving Claire and Marten and their struggles with their relationship. I'm not saying they're going to break up, but when you have two people who are just complete opposites, its going to be tough. Not to mention that Claire's got a bit of a dominant streak that might raise some uncomfortable memories for Marten. And Marten's constant laissez faire attitude to life might be incredibly frustrating to someone with a lifeplan like Claire.
On a related note, the lifeplan Claire has and her seeming unwillingness to be flexible in that respect seems to be setting her up for a major crash back to reality. What happens if she doesn't get a job in a library? What happens when she realises there could be 1000 candidates for one position? What happens if she does get the job and finds it is not what she thought it was going to be? Claire is somewhat tightly wound and that kind of realisation could be devastating.
One last point. Claire is playing with fire right now and she doesn't realise it. Marten might be the most passive character in the comic, but in the past when he's been pushed enough, he's let loose a salvo of some devastating comments about people and their flaws, in particular Faye and Dora. Claire might want to slow down, or she might end up hearing something rather painful.