What were the better options at the time?

Yes, really. There were other reservations about shader compilation in particular from other participants, Apple wasn't alone in that department (e.g. asset sizes and needing to fork the format to maintain compatibility guarantees). They did demand a non-binary format, which sealed the deal on no SPIR-V. But it was not as simple as "SPIR-V/Vulkan was perfect and what everyone except Apple wanted." The shading language by far had the most discussion and iterations; none of the participants in contrast had nearly as many reservations about the structure of the API.