☢The Theistic Response➼ to Atheists saying, "It Doesn't mean God Did it"

[The Joker]

Science has its limits.

Indeed it does...

You can't use a telescope to prove God or get God under a microscope for examination.

Nor can you do any of those for Harry Potter, Darth Vader, The Force, Thor and Mjölnir, etc, etc, etc...

Indeed.

There are many things science can't prove, Science cannot prove that your spouse loves you,

That's debatable...

Science can't prove what I am thinking, right now.

 Science is the only way to really know truth.”

Here, you'll need to define "truth". 
To me, a true statement is one that is an accurate description of reality. So truth would be an accurate description of reality.
Accurate, as far as can be ascertained by all of humanity.

I agree

Thus far, the best objective method to obtain an as accurate as possible description of reality is science.
That doesn't mean that it is the only way, as you say...
Feel free to propose another method and let the brightest minds among our population analyze it for merit.

How could you prove that statement by science?

 
Philosophy?

 Science cannot prove that rape is evil.

 

Here, you need to define "evil".
It's certainly not a pleasant thing to do, when you're the victim, huh?
Empathy allows us to place ourselves on the victim's shoes and reject such unpleasantness.
Or are you wanting to claim that you are without empathy and refrain from raping people simply because there's an old rule book that claims that such a rule is against the wishes of the god therein inscribed?

The resulting trauma tends to produce an unhealthy member of society. And society endures better the more healthy individuals it has, so it leads to a positive balance for society to punish and discourage behaviors that lead to unhealthy individuals.

Atheists, you won't find God that way.

Who said we're searching?

You can’t find God because first of all, they aren’t looking; and second they want to avoid him.

For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable. Romans 1:20 

Science is trying to determine how the Universe works.... how the Universe came into being... if, along that path, a god pops up, then it will be incorporated into science.
If it doesn't (as it hasn't thus far), then it is not considered to be a part of reality - merely a fictional character originating in old old old tales from people attempting to make sense of the world around them.

"Who said we're searching?"

This information was the most important one I ever received from you, Thank You for your honesty, "The Creator is clearly seen," Paul explained to the Romans 1:20. Yet despite all their intelligence and scientific skills, the Gentiles refused to acknowledge the Creator. The problem was not their inability to see Him but their rebellious hearts, which "suppressed the truth in unrighteousness" Romans 1:18. Scripture makes it clear that God’s eternal power and divine nature are clearly seen in the creation of the world around us. God is saying that the design and complexity of nature makes it obvious that He exists. But hard hearts often refuse to accept any evidence that the Bible is true, for it makes them accountable to a Just God the creator of the heaven and earth. For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable. Romans 1:20