A trick I learned from the keychain utility is using one program to build a source-able file containing just the variables that you want to export from your program. You could modify your script to echo the variables you want to set and then source the output from your program:
$ echo $FOO
$ source <(echo FOO=bar)
$ echo $FOO
bar
$
I used echo FOO=bar to simulate the larger script; your program is probably more involved. The important part is that you must modify your program to output the variables and values you would like to set, rather than just setting them. This lets you decide which variables to expose and which ones to hold private at the cost of another shell process.