100% agree. With the current API, there's no real advantage to using Guile over a C extension (other than the choice of language). If the Guile interface could hook into Make's dependency graph, it would be huge game-changer. But as it is, the Guile interface is basically a fancy macro processor.
The Guile interface can expand Makefile expressions into values, and can process/evaluate Makefile statements. But there's no way (that I've found) to do something like "remove this dependency from target X", ask "what dependencies does X currently have?", or ask "do you think X is currently up-to-date?".