[Sanity]

I'm also unconvinced that even several tons of antimatter can cause significant damage to a planet.

You do not need to damage the planet in order to make the inhabitants enemies.

Even a kilo of antimatter exploding will look like a HUGH nuclear explosion. You do not want to dispute why you just did that to them ;) Remember that the biosphere, or the attitude of the peoples are more easily damaged than the planet.

Perhaps the ideal solution would be for the ship to devote an entire module to carrying nothing but pure antimatter, and then a second module that enables it to use this antimatter to create boosted reaction mass, e.g. from ocean water or gas giant atmosphere or comet materials?

I would seriously like to stay away from antimatter if feasible. For a deep space mission the possible negative from any failure is just too hard - i mean, lets ignore the "ship blows up" thing. If for some reason you need more fuel, you just can not get it (maybe you needed to jettison it, whatever). This is ok fo ra military operation (which rarely is a single ship etc.), but not if you go on a deep space exploration mission. Smells like dying in another star systtem, unable to get fuel again.

Plus antimatter is tricky - if contianment fails you die. This can be a problem unless you get passive containment (i.e. a material that contains the antimatter without reaction, not something like a magnetic bottle that constantly needs energy).

It just happens to require expensive equipment, lots of energy input (seeing as antimatter is actually about energy storage, never energy production or energy generation), and take lots of time.

First ppoint - antimatter may be bout energy creation. One of my older sf universes had cheap antimatter production though "misjumps". Certain musjumps let you get out of hyperspace as antimatter - normally resulted in immediate destruction, but you COULD force that in a lap as microjump (i.e. on space), so hugh facilities where build jumping tons of matter in kplace in a controlled misjump to create antimatter - you efficiently got energy out.

You need a similar mechanism, otherwise you will always have EXPENSIVE antimatter, as the energy needs to be generated in the first place ;) Which - is not nice.

Whateve, though, antimatter creation is tricky. You may not be able to get that in place if you need. Better just skim gas giants.