I agree that a naturally occurring wormhole is extremely convenient, I don't deny that.
However an artificially created wormhole has an even longer list of conveniences consisting of:
1) Being made at the right time when our galaxy needs it most.
2) Being made at the right place where our ship/fleet is.
3) Being able to take them to Andromeda safely.
4) Our ship/fleet trusting this random wormhole to be their salvation rather than destruction.
5) The creators of the wormhole having a means to keep an eye on the Milky Way to even know of the Reaper harvests.
6) The Reapers missing this technology for who knows how many cycles.
7) Being closed at the right time so the Reapers don't follow.
Meanwhile like you said a natural wormhole which has the conveniences of:
1) Being made at the right time when our galaxy needs it most.
2) Being made at the right place where our ship/fleet is.
3) Being able to take them to Andromeda safely.
4) Our ship/fleet trusting this random wormhole to be their salvation rather than destruction.
5) Being closed at the right time so the Reapers don't follow.
So while it isn't much less convenient, it still is less convenient for a naturally occurring wormhole to be our means than an artificially occurring wormhole. Besides, this is considering we leave before or during the Reaper War which has no data supporting it.