Assuming arguendo that the TSA baggage screening is a violation of the 4th amend., how are you proposing to ensure airline security, make everyone fly naked?
There are several questions that you are asking here, two of which are: How does one go about mitigating the dangers posed by having large, fragile buildings that are full of fuel flying through the air, and secondly, how does one do this within a constitutional framework?
Addressing the second question first, the problem is that these warrentless searches are completely unconstitutional. The constitution is the supreme law of the land, it clearly spells out what is requried to authorize a search, and these TSA searches are way, way, way outside what is allowed by the constitution.
If it is determined that weaker protections against searches is required, then the only constitutional method to get there is the amendment process. To my knowledge, no such amendment has been made.
I am aware of the rational that, "Air travel is optional. If you don't want to submit to a search, then don't travel by air." I suspect that, if you research the writing of the Framers, that you will find that it is quite clear that among the natural, unalienable rights that are supposed to be protected by governments, is freedom of movement. The above rational is greatly at odds with that right.
Addressing the first question: I don't know that anyone has an satisfactory answer to how to prevent evil people from misusing aircraft. The TSA-style searches clearly are not a solution, as demonstrated by the 9/11 hijackers who succeeded in their efforts by using innocuous-looking box cutters. Since that time, many people have succeeded in boarding airliners with various weapons, both by intent and by accident. I don't believe that the TSA screenings will have any efficacy whatsoever in stopping another 9/11 attack.
I suspect that arming pilots would help.
I also believe that we would be safer if passengers were allowed to carry weapons. Regarding the oft-repeated concerns about a gun battle in an airliner, I have two points. Firstly, the presence of armed passengers would in itself reduce the chance of an incident occuring in the first place, because potential hijackers would be aware that an airliner is now a "hard target", with rather low likelihood of success. And secondly, I'd much rather take my chances in a gunbattle in an airliner than be at the mercy of hijackers. An airplane can take a great deal of damage and still fly, as demonstrated by the number of bullet holes in some of the WWII bombers and fighters that successfully returned home.
I think that reversing the trend towards larger and larger aircraft would help. A plane that's twice the size of a 747 is a much more attractive and devastating target than, say, a 707. (The government could, I believe, properly mandate this change through the authority granted by the Commerce Clause.)