So as discussed in the bug report thread, the reason the anti-missile tech prerequisites are the way they are, is because parts do not have "prerequisites". Once you research a tech, that tech may supply one or more new parts.
I'd like to suggest a possible way to deal with that (edited the topic title appropriately).
I guess my proposal then would be something like viewtopic.php?f=5&t=691
, where the fusion and anti-matter anti-missile parts are provided by "bonus techs" that do not require research, but instead are acquired automatically once all their prerequisites are met.
Of course, in order for it really be a polished idea I imagine there would have to be a bit more GUI support than what I managed to do in my mod. For example, instead of showing "cost: 0" in the research panel for a bonus tech, it should probably replace that line with a short sentence saying something such as "this tech is automatically acquired once all its prerequisites have been met."