This is an old thread, but I just spent a month clarifying exactly this issue for myself (this is the current version of my notes), so I thought I'd share. It's not exactly the question that you asked, but I would like to show that your "usual" expression of Bayes Theorem, is completely well-defined from the measure-theoretic perspective.
For the measure-theoretic description of probability, I found Kolmogorov's original 1933 text (well, the English translation from 1956) to be an excellent reference. It is compact, precise, and everything remains true (although some things can be said more simply by direct appeal to measure theory; measure theory was brand new at the time). Frederic Schuller's lectures on Measure Theory and Lebesgue Integration were invaluable background lessons for me. Billingsley's modern probability text is also a great resource.
To answer the question, it is useful to state the problem a bit more precisely, and to use better notation than, e.g., "$f(x|\theta)$". We are interested in calculating the probability density of a random variable, $X$, with respect to the event that a second random variable, $Y$, takes some value, $f_X\left(x|Y = y\right)$. So, $X$ and $Y$ are real-valued random variables on the probability space $\left(\Omega, \mathfrak{F}, P\right)$, i.e., measurable maps from $\Omega$ to $\mathbb{R}$. By the event "$Y = y$" we mean $\left\{Y = y\right\}$, or, most precisely, $\left\{\omega \in \mathfrak{F} | Y(\omega) = y \right\} $.
For a discrete random variable $Y$, this conditional distribution is perfectly well defined, assuming that $P\left( Y = y\right)>0$:
\begin{align}
f_X\left(x | Y = y \right) &= \frac{{\rm d}F_X(x|Y=y)}{{\rm d}x} \\
&= \frac{{\rm d}}{{\rm d}x} \left[P^{(X)}\left((-\infty, x) | Y = y \right) \right] \\
&= \frac{{\rm d}}{{\rm d}x} \left[ P\left({\rm preim}_X (-\infty, x) | Y = y \right) \right] \\
&= \frac{{\rm d}}{{\rm d}x} \left[ \frac{P\left({\rm preim}_X(-\infty, x) \, \cap \, \{Y = y\} \right)}{P(Y = y)} \right]
\end{align}
where $F_X(x)$ is the cumulative distribution function associated to $X$, and $P^{(X)}$ is the probability measure on $\mathbb{R}$ induced by $P$ (i.e., the pushforward of $P$ under the map $X$).
In standard Bayesian inference, however, one is usually interested in the distributions of continuous random variables, which take uncountably-many values, and for which the probability of a single value is usually zero, i.e., $P(Y=y) = 0$. Therefore, the expression above cannot be used. Instead, we use almost the same notation to define it (compare to the third line above):
$$
f_X\left(x | Y = y \right) = \frac{{\rm d}}{{\rm d}x} \left\{ \left[P\left({\rm preim}_X (-\infty, x) | Y = y \right)\right] \right\}
$$
where the "conditional probability of the event $A$ with respect to the random variable $X$," $\left[P(A|X)\right]$, is assumed to itself be a random variable on $\Omega$ whose expectation takes the value of the associated conditional probability when evaluated over any measurable set $B = {\rm preim}_X(u)$ (with $u$ measureable on $\mathbb{R}$). Kolmogorov shows (Section 1, Chapter 5) that the defining equation for this quantity:
$$
P\left(A \,|\,{\rm preim}_X(u)\right) = \mathbb{E}_{{\rm preim}_X(u)} \left\{ \, \left[P\left(A | X \right)\right] \, \right\}
$$
implies the existence of a unique random variable, which (assuming some continuity conditions) can be written:
$$
\left[P\left(A | X=x \right)\right] = P(A) \,\frac{f_X(x | A)}{f_X(x)}\,.
$$
Using this expression to write the above conditional density, one can easily show that:
$$
f_X\left(x | Y = y \right) = \frac{f_{XY}\left(x,y\right)}{f_Y(y)}\,.
$$
Writing down the analogous expression for $f_Y\left(y | X = x \right)$ and equating the two versions of the joint probability density, $f_{XY}\left(x,y\right)$, leads to:
$$
f_X\left(x|Y=y\right) \, = \, \frac{f_Y\left(y | X = x\right) \, f_X(x)}{f_Y(y)}\,,
$$
which is the desired version of Bayes' Theorem.