<off-topic>
Note: IMHO this is a far more general UI issue. The same conflicts can occur with pattern handles and path effect knots (both types are always stacked on top of the path nodes), but for them there are no workarounds
a) to disable the special knots rendered on top of the path nodes in the node tool context, as well as
b) a special tool to edit the knots only
which exist for gradients.
</off-topic>
<off-topic>
Note: IMHO this is a far more general UI issue. The same conflicts can occur with pattern handles and path effect knots (both types are always stacked on top of the path nodes), but for them there are no workarounds
a) to disable the special knots rendered on top of the path nodes in the node tool context, as well as
b) a special tool to edit the knots only
which exist for gradients.
</off-topic>