It is better to book directly than use a TA that has no high ranking with MSC. Better to use travel agents with the rank "Commander". As your friend said "it appeared the line would just prefer dealing directly with the cruiser instead of an agent" she definitely is no "Commander" ๐
Most important thing is to make a "good" booking. No changes later, book it, pay it, never touch it again. If you have any questions, ask the YC concierge on board, not the hotline. Then the chances are high, that your first MSC cruise will be the best cruise you had so far.