In my opinion, the arguments have not been disproven only that we do not understand the arguments. see the shaar yichud with commentaries
(i.e. we don't study the arguments in enough depth to understand them, therefore we mistakenly think they have been disproven. hence study with the commentaries, and even then if something doesn't make sense, ask wise Rabanim.)
Rabeynu Bachya and the Rambam, etc. are writing to a generation steeped in philosophy therefore, they could present their proofs with minimal introductions. As this does not apply to us, commentaries are necessary.
For example, in the answer by chanoch here: Why is Sha'ar Ha'Yichud of Chovos Ha'Levavos so "controversial"?
it assumes Hawking disproved a premise of the shaar yichud, but if you read the commentaries in the shaar yichud, you will see his disproof was from a mathematical model, whereas the shaar yichud was talking about an "actual infinity", an infinity in the here and now physical world, not a mathematical model.
Furthermore (as a side point), remember science does not have a good track record of being reliable. it is constantly evolving slashing old premises when new ones are discovered but the words of our sages endure forever and ever. (Sefer Habris Maamar 5 ch.3)
As spiritual phenomena is discovered, the entire paradigm of science will eventually collapse and be seen to be merely like a blind men grasping the tail of the elephant as the below quote explains
Ramchal (Mevo L'Sefer Haklalim):
The philosophers and scientists can grasp only the external surface of the world, namely, the physical world, according to what appears to their physical eyes. However, this is merely the outermost garment of the spiritual roots, namely, the sefiros who govern the world and are the innermost spirituality inside the physical... Just like the form of man alludes to the entire system of Divine governance, so too it is alluded from all the parts of nature, and every creation is an expression of one detail of His governance...
And on this are based most of the sayings of the Sages which refer to the Creation and to all matters of the world, whether in heaven or on earth and all of their derivatives, this is also a broad and important subject.
When our sages instruct us on matters of nature and of this world, they are referring to its inner aspect - not on its external garment. Therefore, sometimes in their words we find things which appear strange, and which appear to be clearly false from what we perceive with our senses. But the truth is that they are speaking according to the true governance which is hidden from human eyes, which they received from the prophets and from the holy torah...
(also keep in mind that G-d intentionally created the world in such a way that free will is possible, so there will always be loopholes to interpret the world according to the atheists, otherwise free will is over)
