"Make this work" is usually a positive expression that shows that a person wants to put in the extra effort during a hard situation to find a solution that everyone is happy with. It's a little bit strange in this context, but the speaker is saying that of the two choice he has, he would rather take some time to work on this business partnership before starting to look for a new agency to work with.
People also use it in a very casual way when something doesn't go right, but they want someone else to feel okay about a mistake or something.
For example, if a friend of mine tells me that she'll bring some food to a party, and then she forgets, she might feel bad because there's not enough food for everyone. So, I might say, "We'll make it work" to help her not feel so bad about her mistake.