An alternative for R CMD BATCH is Rscript. I think for problems where C++ and R are not tightly integrated, i.e. there are distinct phases where R and C++ are used, nor large volumes or frequency of data exchange, using system calls can be very simple and robust.
An alternative is to run R and C++ alongside each other and exchange info between them. This can be done using the RInside pacakge, which is available on CRAN.