I have another small VPS, wondering if someone could tell me if I can setup BIND or PowerDNS just to host my second DNS server (ns2)
It is possible. Set up ISPConfig to zone transfer to that ns2 host, where you have installed BIND. Read ISPConfig Manual and/or search for threads in this forum.
Add the IP address of your secondary DNS server in the allow transfer field of the DNS zone in ispconfig. Then configure bind on your second DNS server to act as secondary with automatic zone transfers for the ispconfig server.