Not sure about the above poster, but the only times I've heard folks claim that macports broke their system was when they were setting DYLD_LIBRARY_PATH.
edit
should be noted you really ought not do this and if you absolutely have to you should use DYLD_FALLBACK_LIBRARY_PATH
- MacPorts' /opt/local is not in any of the default system paths.
- MacPorts uses sandboxing to ensure that builds can't stomp anything outside of /opt/local