A bay at Wembley Central is a good compromise, but IMHO the gold standard is platforms at Willesden Junction. Then you possibly don't even need the Southern service at all - you can just use the WLL paths for more Willesden to Clapham LO services, and the WCML slow paths for more services into Euston. Unless there is no capacity into Euston for more services, of course.
The main downside I see at both Harrow and Wembley (and it's the same issue at Watford), is that the terminal bay is always on the outside of the up platform. This means entry into the bay when speed is slowest is a conflicting movement (abet, leaving when you're accelerating away isn't), but more importantly, the cross platform interchange you get is to go back south where you've just come from, not north, where you likely want to continue your journey, making them awkward interchanges.