I kinda don't like the existing answers, so here goes. Let us begin with some pedantic corrections.
controlgroup correctly points out that Bose-Einstein condensates exist. His expression for the limit of the Fermi-Dirac statistics is wrong, though. Let $\theta$ refer to the (symmetric) Heaviside step function, i.e.
$$\tag1\theta(x)=\begin{cases}1&,x>0\\0&,x<0\\\frac12&,x=0\end {cases}$$
then, the Fermi-Dirac statistics tends to
$$\tag2\lim_{T\to0}\tilde n_i=\theta(\mu-\varepsilon_i)$$
i.e. fully occupied ($=1$) below the chemical potential, and completely empty ($=0$) above. He said the function is half in that limit, but that is obviously wrong. That erroneous value would not even be renormalisable: it would have infinitely many particles and all sorts of other nonsense.
However, it will soon become clear that this is only one side of the story.
akhmeteli is also obviously trying to convey a physical fact, but that is expressing it in a rather awkward manner. His claim is also technically wrong; while, yes, composite particles are only approximately handled by coarse-graining their wavefunctions, in particular, treating the extended multi-position constituent wavefunction as just the point-like wavefunction of the centre of mass, but this point-like wavefunction actually has to be boson-symmetric, in direct contradiction to what he claims. It is necessarily so, to obtain the boson statistics.
- The first idea is wrong.
No, the idea is approximately correct. First off, let's be clear with the terminology. Pauli's Exclusion Principle came before we realised that this is coming from fermion statistics, which in turn comes from skew-symmetry of the wavefunction when you exchange particle identifiers. This skew-symmetry causes "free particles" to have what is called degeneracy pressure.
When you actually attempt to quantify the repulsion of matter from penetrating matter, at otherwise zero pressure, you will realise that the contribution from degeneracy pressure and the contribution from the short-range effective repulsion from electrostatic potential, to be roughly the same magnitude. i.e. the kinetic energy increase from degeneracy pressure and the electrostatic potential energy increase from quasi-neutral electrostatic repulsion at short distances give rise to the actual reason why matter does not penetrate matter.
This is not exactly complicated; only the derivation might be. The standard argument as given in textbooks might not be the full picture, but it is pretty much good enough; I mean, you get about half the contribution, which is more than good enough when all you really care about is getting within an order of magnitude.
- Temperature.
This is the only one that is unequivocally wrong. Bose-Einstein condensation happens, and so what you are saying there is entirely wrong.
- The second idea is wrong.
It is also approximately correct. Between controlgroup's and akhmeteli's answers, lies a nuanced answer:
The bosonic symmetry of the simplified wavefunction, only encapsulating the centre-of-mass's degrees of freedom, is an approximation scheme that is wildly successful, but gives the wrong impression that matter would collapse. The correct picture that it captures is that, once you fix the non-centre-of-mass degrees of freedom to just signify the ground state, then, whenever this ground-state approximation still holds as good, then the Bose-Einstein condensation actually can happen. The quantum system can behave as if a macroscopically large number of the molecules have collapsed into one single ground state, exhibiting the collective quantum behaviour that is so counter-intuitive, contrary to classical expectations.
But the underlying reality is still made up of fermions. The fermionic repulsion is still there. This means that, for each additional bosonic composite particle that occupies the ground state, its internal degrees of freedom must occupy higher and higher energy states, e.g. wider and wider momentum pairs, if they are Cooper pairs. You originally had a filling up of states up to the Fermi surface, so this is really just a slight modification of that, even before the electron-phonon coupling, which is so important for creating the Cooper pairing in the first place, starts making the corrections near to the Fermi surface. There is no method at which the Bose-Einstein condensation would result in a collapse, if you consider this properly.
There is another nuance. In QFT, which is what you really need to do to consider interacting systems properly, you will also learn and realise that bosonic fields must have an interaction that has a repulsive core. Or else, the field would not be renormalisable, or that the field would not have a sensible physical interpretation. Sadly, I cannot remember which nice condensed matter field theory book it was that I got to read this fact, but seems to not be in Fetter & Walecka, even though F&W just straight up suddenly discussed the bosonic system with repulsive cores.
Anyway, with these nuances, you should be able to see that quantum theory is not in disagreement with structural stability of matter. At least, until some black hole physics intervenes. Last I heard, we still do not have any physical way to prevent the formation of a black hole singularity, but that is a problem for quantum gravity to solve. We should take the current results as good enough, at least for now.