Assuming you mean this Page Mill Road.
There are no hard and fast rules about manually marking off streets. No CityStrides police will come knocking on your door questioning why you did so. If you don’t feel comfortable running a street for any reason, manually marking off is ok.
As to bigger question of why it’s uncomfortable/dangerous to run (no sidewalk/shoulder, winding blind turns, etc) editing in OpenStreetMap (OSM) would fix in longer term. However, OSM data is used by more than CityStrides so we must all be cognizant of the edits we make and the grander scheme they affect.
For a brief tutorial on editing in OSM, see this page that discusses various things you can do. If you still aren’t sure about making edits yourself in OSM, adding a Note is quick and easy. Another OSM user can review your note and then make edits if needed.
Within OSM, streets are called ‘ways’. A way could be split into different segments/parts. For example, a long street (way) may have different parts with different speed limits. The way could be split and then a different speed limit entered for each segment. Other variables like surface type, number of lanes and more may lead to a way being split into multiple segments. Each segment would have to be edited individually if each part is unsafe to walk/run on.
By default, a lot of the ways get entered as allowing multiple forms of access (foot, motor vehicles, bicycles, horses ). Here is the big long OSM explanation on the different types of access. Personally, I like to think that any road a bike could legally go on, you could also run/walk on. Doesn’t mean the road is bike/run friendly, more it is bike-able and run-able. Subtle difference.
With all that said, one method to fix would be to change the way segments that are not bike/run safe, to have an access of foot=no. Then the next time CityStrides gets updates for the city, those changes would be made in the data. Be aware, if you make the changes in OSM, another person could always change them back because their opinion is different and you’d end up in the same spot you are now. So all else fails, you can still manually mark it.