Fractions or probabilities as training labels
Cross-entropy loss still works with probabilities in $[0,1]$ as well as $\{0,1\}$. Most importantly, $\hat{y} = y$ is still a stationary point (although it will not equal $0$).

It is also the case that the possible improvement in loss (and immediate gradient) is larger for $\hat{y} = 0.99, y = 0.89$ than for $\hat{y} = 0.4, y = 0.5$. If you use a sigmoid output, then the gradient at the logit $\hat{y} - y$ still applies - the larger gradient of the loss function scales inversely to the lower gradient of the sigmoid at that point.

So, in short, yes use binary cross-entropy loss for single-class probabilities, even when they are not strictly in $\{0,1\}$.