I do not see a setting to change the color.
Orange is the new black! Joking aside, it’s a design choice we made, we understand some people will love it, some will be ok with it, and others will hate it. I’m afraid it’s here to stay. We will likely add the much requested dark theme at some point, but will unlikely allow you to make the highlight colour completely customisable.
You’ll be pleased to hear that Agenda for Mac 2.4 now supports both the graphite theme on 10.13 and your preference for accent color on 10.14, the same goes soon for Agenda for iOS as well. This means that if you select a different accent color than the default blue, the buttons in Agenda will adapt this color as well.
An example of Agenda for Mac when having the accent color set to pink in the System Preferences on 10.14 Mojave.