this is what i also think.
as for BIP39 and usage of PBKDF2 i believe usage of this KDF has nothing to do with security. it seems to me that the creators of this BIP wanted a way to let the user store the entropy (which is seen as the set of words) but be able to derive a different BIP32 seed from it and end up with an entirely different set of keys.
to achieve that you'll need a cryptography function that takes two inputs: a data and a salt. there are a lot of options, from HMACs to KDFs. a simple HMAC-SHA512 would have done the same job and an extremely expensive scrypt KDF would have done the same job. but the former would have been too fast and the later too slow. and you have to consider users who wouldn't like it if their initial wallet setup took 1-2 minutes.
since the point was not security but at the same time they wanted to make it a bit expensive choosing PBKDF2 is a good choice in my opinion but as long as people don't see it as a security thing such as a way to encrypt their mnemonic.