I expect the main workflow will be using OpenCL to offload arbitrary work to the coprocessor along with a few Intel-provided modules capable of common tasks.
The great thing about having the FPGA on-die via UPI is that the cache-coherency, decreased latency and massive bandwidth will allow much more granular offloading of work. This is as compared with PCIe coprocessor where it only makes sense to offload larger chunks of work and minimise the communication and data passing between the two.
The greater the granularity of work that we can offload, the more viable the OpenCL/high-level synthesis/heterogeneous computing type stuff will be, as it will integrate more seamlessly into existing software development methods. This is the holy grail at the moment for FGPA vendors: to get to the point where software developers can program them on their own.
As to your point though I guess we'll find out soon what the dev tools for this will actually look like.