What you're saying doesn't agree with physics, however. We clearly see that the energy wave emitted by the Mass Relays being destroyed is, in fact, damaging. It's easy enough to infer from the fact that the Normandy gets damaged.
The entire execution is inconsistent, which presents us with several different problems. But we know that the energy wave is not harmless. Let's assume that, like in [i]actual[/i] physics, mass and energy are relatively proportional. If something can be seen on the galactic scale, it must have a tremendous amount of mass existing as energy. That kind of energy wave, clearly explosive (as opposed to implosive) in quality, would necessarily displace any other mass in its path. So one of three things is happening:
a) We are seeing a molecular movement, which would necessarily mean that all objects near a Mass Relay would be subject to concussive forces, which at that scale would sunder anything unable to sustain the impact. I somehow doubt even the Krogan, nay, the mother of all thresher maws would be up to the task.
b) We are seeing convection, which would cook pretty much everything in the path of the energy wave, provided it could even survive the temperature. Let's assume the average living creature does not have the physical density of the Normandy and it becomes immediately apparent at just how much barbecue is going on.
c) We are seeing a carrier signal effect, which would explain why in some cases it only shuts down synthetics, while it does other things in other cases. However, that doesn't explain the damage to the Normandy. It isn't as if the Normandy is magically closer or farther away from the event horizon.
We're dealing with something clearly destructive, being witnessed on a galactic scale, and even if they didn't cause a nearby supernova, their own impact would be incredibly destructive to all living things nearby.
As to the FTL thing:
Direct distance isn't the issue. It's avoiding all the shit in your path. Basic problem of FTL: Can't go in a straight line. You'll get slagged by tons of debris, could wind up going through a planet, etc. It's even explained in ME's own context as to why the relays are so useful (among other reasons), because of how difficult navigation is due to FTL-related problems.