An alternative reading would say that the editor missed a required comma:
While a malware coder could write code to disable protection in this way, though[,] it would be a complex task.
The use of "though" in that fashion is equivalent to "however", so the sentence could be re-written as
However, while a malware coder could write code to disable protection in this way, it would be a complex task.
(Which means that code-based protection disablement is possible, but it's probably not worth the effort.)
But as @Johnathan Garber points out in a comment, there was already a sentence starting with "However" very close to this one; so the author probably wanted to avoid the repetition. Thus he went with the alternative structure, and then the comma somehow got dropped.
This question seems to be asking about two actions. One is someone 'going through' a backpack. The other one is 'going through the things found in a backpack'.
Stop going through my things
fits the second case.
As does the expression you provided:
Stop searching through my stuff
User3169 has provided a highly idiomatic expression:
Stop digging through my things
CopperKettle has provided the useful verb rummage (which is also a noun):
Stop rummaging (through) my backpack
Also, stop messing with my things/stuff is similar, but it is broader in meaning.
You can also say
Get your hands out of my backpack
Leave my stuff alone
Find your own toys to play with
For variety and vocabulary expansion, you might want to be aware of
Stop rifling through my things
but rifle as a verb means to go through something quickly in order to steal something, and we wouldn't generally use that for a toddler.
Note: I have not used a period after any of the italicized examples, because I want to leave open the fact that you can add , toddler's name or something else the end of each one.
Stop messing with my stuff, lovey dovey.
Best Answer
There's nothing wrong with saying "Take apart your legos*† before putting them back into the box." (Or, equivalently, "Take your legos apart before putting them back into the box.") "Take apart" is a fairly common phrasal verb, and it's about as simple and straightforward a phrase as you can get to express this to a toddler — or anyone, really: it's not baby talk or otherwise condescending, it's just a simple phrase for a simple concept.
*American English usage considers the "lego" to primarily be the block itself, and only by normal pluralization (etc) to be the collection of such blocks. British English is the reverse. Since you put "Legos" in the title of your question, I assume you're using American English, which conveniently is my native dialect.
†As a generic term for a type of block toy, there's no need to capitalize it. The trademark is in all-caps anyway: LEGO®.