Assuming the closure operation you want still gives you a subalgebra of the bounded operators on the same separable Hilbert space, this is impossible in general, since, for example, the algebra of bounded Borel functions on $[0, 1]$ (which is, of course, the spectrum of $C([0, 1])$) doesn’t admit any faithful representation on a separable Hilbert space, as this algebra contains an uncountable collection of mutually orthogonal nonzero projections (say, the projection onto each point in $[0, 1]$).
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As requested, my comments below this answer are incorporated here: If, instead of the algebra of all bounded Borel functions on the spectrum of $A$, we instead want the algebra of bounded Borel functions modulo functions supported on a meager set, and by “closure operation” we mean a closure operator, then as the said algebra is the injective envelope of $A$, we can take the closure of $\Phi(A)$ to be the intersection of all injective subalgebras of $\mathbb{B}(H)$ containing $\Phi(A)$.