It would be helpful if you are more specific into what you are trying to achieve. Currently, there is no implementation in R R, but perhaps other users could provide additional ideas to your problem.
First, if you want to have in R a data frame with the inputs and outputs, it should be straightforward to convert from the FLD to a data frame. For example, from C++, new FldExporter().to[String|File](engine), and then import in R using something like read.csv().
Second, if you want something more controlled in R, you could use the fuzzylite command line, where you specify the engine and then write input values to obtain output values.
Third, you could write an interface using RCPP package to precisely do what you want to achieve, which is still not clear to me.