Your assumption that זרע only means semen isn't correct even in terms of simple biology. A better translation would perhaps be gamete which can be either from the male or the female in terms of offspring. And this is actually how the concept is related in the Oral Torah like Niddah 31a which says in the name of Rabbi Yitzchok quoting Rabbi Immi:
אמר רבי יצחק אמר רבי אמי אשה מזרעת תחילה יולדת זכר איש מזריע תחילה יולדת נקבה שנאמר (ויקרא יג, כט) אשה כי תזריע וילדה זכר
.
The posuk you are quoting is:
וַיְבָרֲכ֤וּ אֶת־רִבְקָה֙ וַיֹּ֣אמְרוּ לָ֔הּ אֲחֹתֵ֕נוּ אַ֥תְּ הֲיִ֖י לְאַלְפֵ֣י רְבָבָ֑ה וְיִירַ֣שׁ זַרְעֵ֔ךְ אֵ֖ת שַׁ֥עַר שֹׂנְאָֽיו׃
In this case, its plain meaning is descendants, not sperm or seed. See, for example, the explanations of Rashi and Sforno who explain that it is the same way that G-d promised Avraham about his descendents.
However, if you are looking for additional, deeper insights, consider what Rabbi Yaacov Tzvi Yolles explains in Sefer Kehilat Yaacov where it says:
זרע הוא סוד המתקת ק״ך צרופי אלהים על-ידי ס״ג
. This is also relating to the kabbalistic concept of sweetening and converting the harsh and bitter judgements via what are called the feminine brains (מוחין דנקבה 63 ס״ג).
That in general, the source of the gamete is from the brains as it is discussed in the Torah literature. And so in the context of the posuk from the Torah, the Gates of His enemies is referring to those harsh and bitter judgements which will be sweetened via the feminine intellect which is associated here with Rivkah.
But it is important to note that this is only when Rivkah is joined with her husband, Yitzchok like is emphasized by Rabbi Yolles beginning with the words:
רבקה המלכות נקראת כן אמנם לא תקרא כן אלא מצד תוקף ומתייחדת עם דודה כו׳