וַיָּבֹאוּ עַד-נַחַל אֶשְׁכֹּל, וַיִּכְרְתוּ מִשָּׁם זְמוֹרָה וְאֶשְׁכּוֹל עֲנָבִים אֶחָד, וַיִּשָּׂאֻהוּ בַמּוֹט, בִּשְׁנָיִם; וּמִן-הָרִמֹּנִים, וּמִן-הַתְּאֵנִים.
לַמָּקוֹם הַהוּא, קָרָא נַחַל אֶשְׁכּוֹל, עַל אֹדוֹת הָאֶשְׁכּוֹל, אֲשֶׁר-כָּרְתוּ מִשָּׁם בְּנֵי יִשְׂרָאֵל.
And they came unto the valley of Eshcol, and cut down from thence a branch with one cluster of grapes, and they bore it upon a pole between two; they took also of the pomegranates, and of the figs.
That place was called the valley of Eshcol, because of the cluster which the children of Israel cut down from thence.
The midrash Rabba on Shlach says:
לַמָּקוֹם הַהוּא, קָרָא נַחַל אֶשְׁכּוֹל, זה שאמר הכתוב, מַגִּיד מֵרֵאשִׁית אַחֲרִית, שהכל צפוי היה לפני הקדוש ברוך הוא. אשכול אוהבו של אברהם היה, ונקרא אשכול על אודות האשכול שעתידין ישראל לכרות ממקומו
Basically, the midrash cites a pasuk in Yeshaya 46:10:
מַגִּיד מֵרֵאשִׁית אַחֲרִית, וּמִקֶּדֶם אֲשֶׁר לֹא-נַעֲשׂוּ; אֹמֵר עֲצָתִי תָקוּם, וְכָל-חֶפְצִי אֶעֱשֶׂה.
"Declaring the end from the beginning, and from ancient times things that are not yet done; saying: 'My counsel shall stand, and all My pleasure will I do'; "
to show that Hashem knows what will happen in the end, from the beginning. Eshkol was a friend of Avraham (and that is why he called it the valley of Eshkol), and it was called Eshkol (Hashem arranged that it be called such) because of the Eshkol=cluster of grapes that the Jews would eventually take from there.
How do we know Eshkol was Avraham's friend? We can look at Bereishit 14:24, where the king of Sodom offers Avraham spoils of war, and Avraham refuses, but tells him to give to those who went with him to war:
בִּלְעָדַי, רַק אֲשֶׁר אָכְלוּ הַנְּעָרִים, וְחֵלֶק הָאֲנָשִׁים, אֲשֶׁר הָלְכוּ אִתִּי: עָנֵר אֶשְׁכֹּל וּמַמְרֵא, הֵם יִקְחוּ חֶלְקָם.
"save only that which the young men have eaten, and the portion of the men which went with me, Aner, Eshcol, and Mamre, let them take their portion.'"
Anyway, the midrash is answering the issue of dual etymology. Since Eshkol was a contemporary of Avraham, it would make sense that a place names Nachal Eshkol from that area would be called that, especially since Mamrei was another of these friends of Avraham, and there was a place called Elonei Mamrei.
The midrash seems to be reading the pasuk thusly:
לַמָּקוֹם הַהוּא, קָרָא נַחַל אֶשְׁכּוֹל - to that place, Avraham (or Hashem), in the past, called Nachal Eshkol, עַל אֹדוֹת הָאֶשְׁכּוֹל, אֲשֶׁר-כָּרְתוּ מִשָּׁם בְּנֵי יִשְׂרָאֵל, also because of the Eshkol that the Jews (switch here from past כָּרְתוּ to future שעתידין לכרות) would cut from there.
Update: Come to think about it, the dual etymology is probably not the problem here (since there is nothing to force the dual etymology), but rather the answer. The problem is more likely that the previous pasuk calls it Nachal Eshkol (and they arrived at Nachal Eshkol) and then we read that they took an action that led to the place name. This implies that the place had this name before they arrived there, and the answer is that it indeed did.