We can infer some general topological properties of the system for special cases. This has been used in the recent "trending topic" of condensed matter physics, topological insulators. For simplicity, I will restrict myself in the following to $2\text{D}$ systems although one can generalize everything to $3\text{D}$.
The time-reversal operator is an antiunitary operator that admits the following representation:
$\hat{\Theta} = \exp \left(i\pi\hat{S}_y/\hbar \right)K$
where $K$ means complex conjugation and $\hat{S}_y$ is the spin operator along the $\hat{y}$ axis. Consider a fermionic Hamiltonian for spin $s=1/2$ electrons. Then
$\hat{\Theta} =-\hat{1}$ [*]
In this case, Kramers theorem applies:
Let $\hat{\mathcal{H}}$ be a $T$-invariant (fermionic) Hamiltonian. Then,
all the eigenstates of the Hamiltonian are twofold degenerate.
The proof of this statement is simple once you have understood [*]. As a consequence, $T$-invariant fermionic systems must have topologically protected
twofold degenerate states. The $T$-invariant Hamiltonian satisfies
$ \hat{\Theta}\hat{\mathcal{H}}
(\mathbf{k}) =\hat{\mathcal{H}} (-\mathbf{k}) \hat{\Theta}$
and can be classified by a new topological index, called the $\mathbb{Z}_2$ index. The $\mathbb{Z}_2$ index, $\nu$, is an integer
given by the number of edge states modulo $2$ and distinguishes the $\nu = 0$ or insulating phase from the $\nu = 1$, the topological insulator. Thus, the equivalence classes of $T$-invariant Hamiltonians for insulators can be classified by its $n = 0$ Thouless-Kohmoto-Nightingaleden Nijs invariant [i.e. its $C=0$, first Chern index] and the additional index $\nu$. This gives a $\mathbb{Z} \times \mathbb{Z}_2$ symmetry for the $2\text{D}$ band structures.
After all, what can we infer from the Hamiltonian? For example, that we have time reversal invariant electronic states with a bulk electronic band gap that supports the transport of charge and spin in gapless edge states. This is exactly what we get in the so-called quantum spin Hall phase.
If we define $\mathcal{T}=i\sigma_y K$ where $K$ is complex conjugation, i.e.
$\mathcal{T}\psi_\uparrow \mathcal{T}^{-1}=\psi_\downarrow, \mathcal{T}\psi_\downarrow \mathcal{T}^{-1}=-\psi_\uparrow$,
Then naively a term like $\Delta e^{i\Phi}\psi_{\uparrow}^\dagger \psi_{\downarrow}^\dagger$ is not invariant under $\mathcal{T}$. This is basically the problem you encountered, phrased a little differently. However, it does not mean that the system actually breaks $T$, as all physical observables will be invariant under $\mathcal{T}$. The resolution is in the definition of the transformation of $\psi$ under $\mathcal{T}$. Let us modify the definition to be
$\mathcal{T}\psi_\uparrow \mathcal{T}^{-1}=\psi_\downarrow e^{-i\Phi}, \mathcal{T}\psi_\downarrow \mathcal{T}^{-1}=-\psi_\uparrow e^{-i\Phi}$.
This phase is not observable (it is essentially redefining the phases of the basis states of the second-quantized Fock space, which has no consequences on physical observables), so we are free to do so. Notice that the important algebraic relation $\mathcal{T}^2=-1$ (for the classification of TI/TSC, etc.) is not affected. Then the pairing term is invariant.
Of course, this only works when $\Phi$ does not depend on positions. Otherwise (e.g. when there is a vortex) one can not get rid of the phase, since $\nabla\Phi$ is an observable, the supercurrent.
Best Answer
A time reversal operator is an anti-unitary operator, which can be expressed as:
$\mathcal{T}=UK$
where $K$ denotes complex conjugate and $U$ is a unitary operator. In case of spinless particles, $U$ is chosen to be Identity. Thus $\mathcal{T}=K$.
If the system has $\mathcal{T}$-reversal symmetry:
$$ KH\psi=HK\psi $$
which leads to:
$$ H^*\psi^*=H\psi^* $$ meaning that the Hamiltonian must be real symmetric.