I will point out that Physics and Chemistry are awarded by the Royal Swedish Academy of Sciences while the Peace Prize is awarded by a separate Norwegian committee, so it is plausible that one would be more respectable than the other. Literature is a completely different institution as is Physiology/Medicine.
The Peace prize and Literature prizes have far more questionable winners in my view than the Physics and Chemistry ones.
Economics wasn't added until the 1970s, and has had some extremely suspect winners.
For now, this is not so much about being "respectable", as about the prizes given in the Sciences are not so bound to ideology or politics.
AlphaFold/AlphaProteo is genuinely a major breakthrough in biochemistry. Now if they start to hand out prices in Physics, say, based on it's importance in promoting some specific ideological agenda, then I would be wary. (For instance if they give the price in Physics for "making the the field of Physics more relatable to transwomen in the Middle East".
Some people see it as obvious that hard science and politics have glaring differences that makes the meaningfulness of an award for being very good at one or the other very different.
The Nobel committee picks candidates for all the prizes, and the final decisions are split up over four different institutions.
The only argument I could see along these lines would be favoring the Royal Swedish Academy of Sciences in particular, but that would mean that chemistry, physics, and economics count but medicine doesn't count. And that's just confusing.
