This is an issue that seems to keep coming back to haunt us on various projects where we have to embed web content within a Windows Phone application. One of the best solutions is to modify the CSS of the page being displayed to disable the touch behaviour using the –ms-touch-action (noted that whilst in IE11+ the recommendation is to use the touch-action property but for WP the vendor prefix is still required).
One of the team that I work with came across a post by Colin Eberhardt that handles some of the manipulation events in the visual tree surrounding the actual web content, thereby disabling the pinch-to-zoom behaviour. This technique makes use of Linq to XAML/Visual Tree which is also worth a read