Well, I think it would depend on what type of unit it is and what sort of role in the game you want it to have.
For example, a V2 is a big unmanned strategic missile, and not really reloadable or tactically usable. It has a ground crew, but they only set up and fuel the missile when it is delivered. So the current system of a one-way switch into a kamikaze is a good implementation. These one-use units are also very suitable as auxiliary units or special 'gifts' from high command.
Units which have a more 'reloadable' or 'reusable' character might be treated differently. I'll try to use some of the weapons you mentioned as examples, note that a 'rocket' is normally unguided, and a 'missile' has some form of guidance or way to correct its course after launch:
V1 & V2: one-shot, unmanned, strategic use missiles. So these are fine the way they are, a ground launcher switching into a kamikaze missile.
Mistel: this could be treated the same way, but it starts out as a (tactical) bomber with no attack, and switches into a kamikaze.
Hagelkorn: I assume you mean the unguided model, this will be a bit more difficult, as it is simply a large, long-range, very inaccurate bomb being dropped by a bomber. So maybe a special bomber unit that has a ranged attack or something? So no switching necessary, unless you want to switch the bomber unit from a 'normal' mode into a 'ranged' mode or something?
For these types of gliding bomb, the Fritz-X is already modeled in the game in one GC scenario, as a special bomber, and the Hs 293 could be modeled like this as well. This would also work for the 'Ruhrstahl' (X-4), as it has very short range. So a high INI and low ammo could help portray it.
Enzian, Rheintochter & Wasserfall: short ranged, so could be a 'normal' AA type unit, no need for switching I think. Were these things only guided by hand from the ground, if I remember correctly? BTW, these AA missiles are useless against low-flying aircraft, or when used at very close range, they would have needed extra Flak support to keep the fighterbombers from picking them off.
Rheinbote: weak long-range artillery unit, no switching. It's just an unguided artillery rocket with good range and horrible accuracy and payload.
Natter: this one is more tricky, it is semi-reusable, has a pilot and is more of a tactical unit. A bit like a Me 163 rocket fighter, but it was supposed to be launched from a small tower, cheaper and it can't land but parts (and pilot) can be recovered and re-used. Mmmh...
Maybe a switchable ground 'launcher' unit, it switches into a fighter with the 'missile' trait, so it can't refuel, and can be switched back into the ground unit in order to refuel it? I'm not even sure that would work, but it would be the best I can think of right now.
As for rate of fire, reloading time, it would depend a lot on the type of weapon and the stats. For a rough impression, here is an old movie about cold-war US artillery systems, where you can see the difference in setting up and loading an artillery gun and what it takes for a small tactical artillery missile like the 'Little John' (21m34s) and a bigger 'Honest John' (at 24m48s). A 'Pershing' is also included at the end, which would be more like a V2 equivalent.
http://www.youtube.com/watch?v=3qnRTAyN92M
And a similar comparison between heavy AA guns and AA missiles, this time from the Soviet Union, at 2m40s a demonstration of loading an S-75 AA missile (NATO SA-2 'Guideline') and an S-125 (SA-3 'Goa') missile battery at 5m35s, with the radar firing sequence at 7m12s and optical tracking mode at 8m48s. It makes a nice comparison with the AA guns at the start of the video, I think.
http://www.youtube.com/watch?v=rD94O2nPNCA
