Unless your battery was completely dead, hooking it up backwards would not fry anything except possibly the charger which would happen inside or outside the boat if it didn't have reverse polarity protection which most modern chargers have.
Leaving the battery in the boat is fine.
SeaDoo in particular advises against charging in the boat. I know of at least one person that fried the ECM when he hooked the battery up backwards. Its dark down in the battery compartment so its not impossible.
Maybe other "boats" are different. Regardless, better to be safe than sorry. At the very least, disconnect it.
I have 7 batteries I charge over winter, with 3 different chargers. One is an oldie from the 1960's. It still does the job, so why get rid of it. I'm sure it has no RP protection. Since others may have old junk like that, they need to be careful, not just think it might be fine.