Hi pillemann!
Yep, you are completly right. I changed it to ALT_LEGACY_INTERRUPT_API_PRESENT and voilá it works. The errors are gone and I also noticed a warning which states "implicit declaration of alt_irq_register();" disappeared. This seems logical since it's also a legacy function.
I also thought about using the VIC as an EIC but I 1st wanted to check this "version" of IRQ interuption. Maybe I'll also (have to) use the VIC later.
My first ideas for your problem would be to set the non-interruptible IRQ to highest priority or to disable all other IRQ's while inside the ISR. But I guess you already thought about this :P