Tough to argue that in my mind. As for protein, you could try to increase more natural sources of protein, especially the natural kind, such as wild-fish, organic / free-range products etc. Personally, I wouldn't worry about protein powders in shakes - but double check on your brand (you're not being cheap, huh?).
Your HDL/Cholesterol ratio is not too shabby IMHO (HDL of 50 is quite respectable in fact), but your Doc is spot-on to raise any elevation of total cholesterol as an area of interest / concern.
Taking out other products at this time is unlikely to do harm, so I would heed your Doctors advice and let time do it's thing; and provide the evidence required for an informed opinion. You can always restart taking a supplement; you can't always undo harm-done.
Also, have you changed your exercise routine significantly? It too can affect cholesterol and hormone levels quite significantly.