The aegis security checks the hashes of the binaries, and compare them to authorized ones. It will prevent you from running your non Nokia signed version, even as root (permission denied), and will prevent the system from running it during boot (bricked device). If you don't need too many privileges for obexd, you can try to package your custom version, and install (dpkg) it in devel mode (which may get aegis to register and trust the binary). If this needs privileges restricted to Nokia, then you won't be able to change the obexd without using a custom, aegis-free kernel. See there for details.
A lot of work has been put to better interoperability of BT with cars. I don't know of the exact model you have, but likely the situation is better in PR1.1