Technically, if you read the scan you provided, it doesn say she can't be directly harmed by HER manifestations. What is says is none of the weather's manifestations can directly harm her.
Read it again:
http://2.bp.blogspot.com/ygn5s7GAPlq...2rstW8lc=s1600
"Her mutant gift is to control the weather. None of
IT'S manifestations can directly harm her." So, the War Machine thing was PIS.
Going on from that, let's look at instances Claremont wrote where the lightning did hurt Storm (Uncanny X-Men 150):
http://2.bp.blogspot.com/wBSHk1E812g...bT016cdl=s1600
In the scan above, it states that the only reason she was hurt by the lightning is because it caught her by surprise. Now, let's look at something else Claremont wrote (Uncanny 104):
http://2.bp.blogspot.com/l8Qj0yh7OrR...U7L5CUrJ=s1600
In the scan above, Storm clearly knew the bolt was coming at her, so she was not caught by surprise, yet it still hurt her. Can
everyone see how this from Uncanny X-Men 104 contradicts the scan from Uncanny 150?
Then there is canon that states none of the weather's manifestations can directly harm her as shown in the scan from Uncanny X-Men #168.
In other words, Claremont was all over the place. In some stories, she was immune to lightning, whereas in others, she was not. It all depended on how he felt at the moment which made for some bad PIS instances. It doesn't make any sense for her to be harmed by lightning, to be honest, so Pak came along and established definitively that lightning cannot hurt her.
Now, getting back to the instance where she was caught off-guard in Uncanny X-Men 150, there was loads of other PIS to be considered there. In order for Magneto to bring that bolt on top of Storm's head like that, he had to create a magnetic field above her (which is what he even states he did). Storm should have been able to sense the concentrated field above her head since it was established before this story that she can do stuff like this:
http://2.bp.blogspot.com/H7XyGpnHcfu...rc_uq4Bi=s1600
Notice in the scan above, she was able to track down the faint traces of the energy trail Vendicator's suit left in the air when he flew through there hours earlier.
Also, she can detect all natural occurances before they happen (Uncanny X-Men 118):
http://2.bp.blogspot.com/IIHhgkOFhTs...MuFd5q1S=s1600
In other words, she should have felt that lightning bolt in Uncanny 150 before it came into being, meaning it should not have been able to catch Storm by surprise to hurt her.
Pak deserves applause for what he did. He took the sensible route and simply made Storm immune to lightning, as she should be.