What options are there for rebuilds of indexes on large tables for a data warehouse?
At 4 vCPU you're on the smallest Enterprise Edition, so your cost isn't prohibitive. You will need to keep up to date with the Software Assurance if you want HA on your VM.

I would recommend adding memory to this (assuming its available in the hypervisor) and taking this VM to the maximum that edition of SQL can support (64GB for 2008 R2). That's probably your lowest cost option.

If that doesn't give what you want / need then realistically you are looking at Enterprise Edition and table partitioning to manage the data which isn't being manipulated by the ETL. 

If the majority of the data isn't being changed, and it just gets reloaded time after time, then that needs to change as its not going to be sustainable. Only load the data which needs to be reloaded.