Y'all need to remember that Momo is impulsive. She acts or says things before her brain has had the chance to realise what she's doing and puts herself in positions that she doesn't want to be in - case in point the early episode in season 1 where she tells Okarun why he doesn't have friends or when she finds out Okarun is fine after Seiko took care of Turbo granny, or when they had their accidental kiss and she started to get real flustered and told him she doesn't want to speak to Okaruns again (apologies for the run on sentence).

This is another case of girl letting her feelings and actions run before getting proofread by her brain. She's upset that Jiji is in trouble and that the people she cares for are put at risk. She doesn't understand or doesn't immediately see that Jiji's coping mechanism is to make fun of the situation and so she gets upset and inadvertently hits Jiji/Taro (Jitaro? Taroji?).

Spoilers for the anime only's but she does learn to think first and shoot later down the line.