In case anyone was curious, the one way you can prevent Marathas from launching naval invasions (short of destroying them) is just blockade their ports. It's much cheaper than garrisoning every region you own, especially in the Carribean. This makes excellent sense for any faction that is trade good rich and wealthy land poor. Such factions (like GB) will benefit most from control of the seas (and trade nodes) and can also keep land force costs down by simply blockading all ports of enemy factions.

Marathas is so badass because they have the 2nd best strategic position in the game and I'm guessing their units must be superior to those of the Mughals because they take over India EVERY time. The Mughals have to worry about Marathas, Mysore, and Persia or Ottomans. Marathas just have to worry about Mughals and Mysore. Marathas also have TONS of ports whereas the Mughals seem to only have one.