How about eval_pv'ing a string containing the contents of the file, plus "DynTrans->import;"? use DynTrans; is roughly equivalent to BEGIN { require DynTrans; DynTrans->import; }. eval_pv'ing the contents of DynTrans.pm is like require-ing it. Add a "package main;", before the import, and voila!

Tested this, and it works:

Key lines:

/* moduletext = text of module + "package main; DynTrans->import;" */
    eval_pv(moduletext, TRUE);         /* ~ use DynTrans; */
    eval_pv("$a = fortytwo();", TRUE); /* its function is available */
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Full C source

#include <EXTERN.h>
#include <perl.h>
static PerlInterpreter *pi;

/* Note the last two lines "package main; DynTrans->import" */
static char *moduletext =
"package DynTrans;\n\
use base qw/Exporter/;\n\
our @EXPORT;\n\
BEGIN { @EXPORT = qw/&fortytwo/; }\n\
sub fortytwo { 42; }\n\
1;\n\
package main;\n\
DynTrans->import;";

int main(int argc, char **argv, char **env) {
    STRLEN n_a;
    char *embedding[] = { "", "-e", "0" };
    pi = perl_alloc();
    perl_construct(pi);
    perl_parse(pi, NULL, 3, embedding, NULL);
    PL_exit_flags |= PERL_EXIT_DESTRUCT_END;
    perl_run(pi);
    eval_pv(moduletext, TRUE);         /* ~ use DynTrans; */
    eval_pv("$a = fortytwo();", TRUE); /* its function is available */
    printf("EXPECT: a = 42\nGOT:    a = %d\n", SvIV(get_sv("a", FALSE)
+));
    perl_destruct(pi);
    perl_free(pi);
    return 0;
}
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OUTPUT:
EXPECT: a = 42
GOT:    a = 42
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