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Well the problem with orbital bombardment is it is a costly endeavor and... depending on the munitions dropped upon the planet then there may not be a planet left to colonize.

Orbital bombardment is ineffective unless employed en-masse against an enemy who has a fixed position. But even then there are structures not only know to resist orbital fire, but also have enough fire power to shoot space born threats out of the heaves. Just look at the Vraks campaign, which could've easily been won if not for a massive amount of well-fortified laser silos.

Plus, glassing a planet in the Emperor's domain is a rather crude and heretical point of view. It is far better that the blood of a million martyrs stains the soil then that you destroy it forever.

Also, Guard and Navy are two separate entities, with a strong and hostile enmity running between the two.

PDF is first line of defence, when invaded, a call for help is issued via astropath. Marines may be deployed if available, and are fastest to get there, with fast ships and battle-ready forces. If they are unavailable or not enough to deal with threat, IG regiments are raised from nearby worlds and sent by naval transports. Navy is usually restricted to mainataining space superiority, supply transport etc. - orbital strikes are hugely inaccurate, and Exterminatus is sole domain of the Inquisition, as inhabitable planets are priceless in the Galaxy.
For RL example, Germany was bombed heavily in WW2 but it took ground invasion to force defeat.

Gotta disagree there, the Inquisition has vessels capable of firing the required viral and cyclone torpedos.

Capability, but not the authorization. An Inquisitors Ship may be able to carry, maintain, and use the weapons but they are not allowed to because they would have to much power and reckless Inquisitors would annihilate worlds for no reason.

Only a Battle-Barge of the Adeptus Astartes may carry and fire Exterminatus weapons, when given the order by an Inquisitor.

Trust me, I used to adore the Inquisition BHS, and I've tried to find every scrap of info I can on them, when I was younger that was.
There is no law above the Inquisition, except the Emperors and the Adeptus Custodes (As I remember.). Space Marines can be used by any Inquisitor via ancient pacts or deals made, but not controlled, as stated in Dawn of War.
The Inquisition black ships are the ultimate authority in Space ranking, except Space Marine ships of course.
A Inquisitor may get control of a Black ship, but he would have to file a report to the Inquisition enclave at the nearest HQ, when he does, he can fire, or if he needs to, fire, then do the report.
Eventually though, if a radical bombs planets are random, the Inquisition will find out about it, and make the ship detonate, by failsafe detonators planted in the ship.

You have to remember, there isn't as many crazy/heretical Inquisitors as the books and fluff portray, extremely radical Inquisitors are very rare, while radicals are less rare, then Puritans are the most common.

No, Black Ships are not combat vessels. But the Inquisition has other vessels at their disposal.

And Lexicanum is a great big pile of non-canon s**t. Except for some of their marine articles, which are direct copy-paste actions from old IA articles.