The general rule is that letters "בגד כפת" do have a dagesh when they appear in the beginning of a word, unless the word follows a word that ends with one of the vowels (אהוי), and there's a contextual connection between the two words (for example, "אחרי כן").
So here, by saying "כרעותיה" without a dagesh, you are actually saying that the two words "ברא כרעותיה" are connected, which means "[that He has] created according to His will".
This sounds right, but the Vilna Gaon actually says that the "כרעותיה" is not connected to "ברא", but to the beginning of the kadish ("יתגדל ויתקדש... כרעותיה") - i.e. that He will be praised according to His will. So there should be a slight pause between "ברא" and "כרעותיה", and therefore the "כ" has a dagesh.
Notice that a proof for the Gaon's way is the following prayer we say on Shabbat:
עַל הַכּל יִתְגַּדַּל וְיִתְקַדַּשׁ וְיִשְׁתַּבַּח וְיִתְפָּאַר וְיִתְרומַם וְיִתְנַשּא שְׁמו שֶׁל מֶלֶךְ מַלְכֵי הַמְּלָכִים הַקָּדושׁ בָּרוּךְ הוּא. בָּעולָמות שֶׁבָּרָא הָעולָם הַזֶּה וְהָעולָם הַבָּא. כִּרְצונו וְכִרְצון יְרֵאָיו וְכִרְצון כָּל בֵּית יִשרָאֵל.
The source for this prayer is Sofrim 14, 12, where it would seem that it couldn't be that "וכרצון יראיו" is connected to "ברא", but to the first part of "יתגדל" etc.