Hm... Animating the Lemon-Bridge is likely to be... interesting. Doable, thanks to the ship-sprite-replace method, but interesting. The first question, of course, is why it doesn't just fly into battle with guns deployed; my suggestion would be that having the guns active, say, reduces top speed / maneuverability, and the LB's ship system is used to indicate when to deploy/hide weaponry.
The second question is, are those supposed to be turrets? If so, things just got more complicated; you'll need a way to hide the weapon sprite, and a last frame of animation where the guns vanish from the ship sprite (to be replaced with un-hidden weapon sprites). Pretty sure this is all doable, just a bit complicated. Oh, and you'd need to make sure to set the guns to straight forward, and to have de-activating the ship system rotate the guns back to straight forward before re-folding everything.
You'll also need a way to make sure the player can't fire those guns unless the system is active; again, doable - I'd be inclined to do something like have the ship system when off increase ballistic (the turret up front is energy, right?) flux costs by 1000%, but it should be possible to just disable them instead.
So... Yeah, all totally doable.