The onus of docking with the refueller in a probe-and-drogue system is on the pilot which means that he himself needs to manoeuvre his aircraft and in result the probe into the drogue basket, which at those speeds and altitudes is like threading a needle. So for this the pilot needs to keep constant watch on the probe and have clear view of his flight instruments at the same time. This means that the probes' ideal position would be some where in-front-ish of the pilot which would also mean the probe partially obstructing the pilot's view, there is no other way around it. Hiding the probe closer to the nose and out of the pilot's sight is out of the question. The only way a probe-and-drogue system can avoid this completely is by having a retractable probe, which for certain reasons we do not have on the JF-17.
However, the fixed probes aren't a big deal either. Let's not forget that all pilots do already deal with the canopy strut obstructing their view (except on the F-16 and the F-22),
Mig-29:
F-15:
You can think of the probe and the strut as the pillars besides the windscreen of your car. They obstruct vision almost directly in front of you but as soon as you gain some experience driving that car you don't even notice them any more, it's as if they aren't even there,
This is because our brains are wired to disregard redundant visual data making it virtually invisible e.g. our noses are always visible to our eyes but our brain chooses to ignore them (Although this is the best case example due to our bifocal vision's proximity to our nose). Or when something like this happens,
Btw, Rafale's probe is in an even more obstructive position than the JF-17's; almost in front rather than towards the side like the JF-17's. So if the Rafale's ok with its probe, our Thunder will be just fine.
In a flying boom refuelling system however, like that on the F-16, the responsibility of docking the boom with the aircraft is on the dedicated boom operator sitting in the refueller. Hence all the pilot basically needs to do is fly as steady as he can while the boom operator manoeuvre's the boom into the fuel receptacle of the aircraft being refuelled. This allows the fuel receptacle to be anywhere e.g. behind the pilot.