I'll start by saying I am not familar with IronJacamar.
But from CDI standpoint, you would need to start the container yourself. This is perfectly fine as Weld allows you to do that (Weld SE, which in fact is a "start yourself" standalone container).
But to my knowledge, there isn't a way to do this with EJB which is the real problem here.
I suggest you raise this question on IronJacamar forums, as this is more of an IJ question than Arquillian.
To get this issue solved i packed my rar into a Arquillian test running Wildfly. This was more painful to get started but has the advantage of getting full integration testing on a real container.