Gilgul and the Bavli

Theres a long running dispute in Judaism with the rationalist school of thought on one hand and the kabalistic one on the other regarding if the notion of gilgul neshama has a legitimate place in yahadus. 

The Talmud Bavli does not explicitly weigh in on the issue. 

However, implicitly, it apparently does. 

Bava Metziah 107a states ברוך אתה בבואך וברוך אתה בצאתך שתהא יציאתך מן העולם כביאתך לעולם מה ביאתך לעולם בלא חטא אף יציאתך מן העולם בלא חטא with רש"ש famously commenting מכאן סתירה קצת לבעלי דעת הגלגול by which he means that if ones takes up the belief in gilgul then how can the talmud say that he was clean of sin when he was born as perhaps he is a gilgul that is here to rectify an issue from a previous life. Rashash says that it's only a minor problem by which he is apparently alluding to the deflection that the gemara can possibly be referring to the souls initial descent when it was still unsullied. 

In any case, he was roundly attacked by the faithful for daring to suggest that the Bavli might not subscribe to the concept of gilgul neshamah which occupies an extremely prominent place in kabalah. Rumor has it that some diehards refuse to study his work due to that "irreverent" comment.

If Rashash found a gemara that he thought presented a small problem to the pro gilgul camp I think I've located a couple of passages in maseches berachos that would seem to present an even tighter case for the Bavli's rejection of gilgul, they are:

5a

אֲמַר רָבָא וְאִיתֵימָא רַב חִסְדָּא: אִם רוֹאֶה אָדָם שֶׁיִּסּוּרִין בָּאִין עָלָיו, יְפַשְׁפֵּשׁ בְּמַעֲשָׂיו, שֶׁנֶּאֱמַר: {איכה ג':מ'} "נַחְפְּשָׂה דְרָכֵינוּ וְנַחְקוֹרָה וְנָשׁוּבָה עַד ה'⁠ ⁠"; פִּשְׁפֵּשׁ וְלֹא מָצָא, יִתְלֶה בְּבִטּוּל תּוֹרָה, שֶׁנֶּאֱמַר: {תהלים צ"ד:י"ב} "אַשְׁרֵי הַגֶּבֶר אֲשֶׁר תְּיַסְּרֶנּוּ יָּהּ וּמִתּוֹרָתְךָ תְלַמְּדֶנּוּ";

וְאִם תָּלָה וְלֹא מָצָא, בַּיָּדוּעַ שֶׁיִּסּוּרִין שֶׁל אַהֲבָה הֵם, שֶׁנֶּאֱמַר: {משלי ג':י"ב} "כִּי אֶת אֲשֶׁר יֶאֱהַב ה' יוֹכִיחַ".

Now, even if one can't detect any sin or even bitul Torah to pin the yisurin on, how can one ever conclude that they are afflictions of love if there is always the possibility that they are payback for a previous incarnation's misdeeds? 

Apparently gilgul is not a valid option. 

7a

אָמַר לְפָנָיו: רִבּוֹנוֹ שֶׁל עוֹלָם, מִפְּנֵי מָה יֵשׁ צַדִּיק וְטוֹב לוֹ וְיֵשׁ צַדִּיק וְרָע לוֹ, יֵשׁ רָשָׁע וְטוֹב לוֹ וְיֵשׁ רָשָׁע וְרָע לוֹ?

If gilgul is an option then what was Moshe's problem; the first is perhaps a fresh soul that is righteous; the second a recycled one that is good now but misbehaved in a previous incarnation and has a debt to pay; the third is also a gilgul that just came back to rectify some small stuff and then went bad but is still overall a righteous soul; and the last is a fresh soul that is sinful and doesnt have any merits in its history.

It doesnt seem that Moshe factored gilgul into the equation acc to the bavli

58b 

אָמַר רַבִּי יְהוֹשֻׁעַ בֶּן לֵוִי: הָרוֹאֶה אֶת הַבַּהֲקָנִים, אוֹמֵר: "בָּרוּךְ מְשַׁנֶּה הַבְּרִיּוֹת". מֵיתִיבִי: רָאָה אֶת הַכּוּשִׁי, וְאֶת הַגִּיחוֹר, וְאֶת הַלַּוְוקָן, וְאֶת הַקִּפֵּחַ, וְאֶת הַנַּנָּס, וְאֶת הַדַּרְנִיקוֹס, אוֹמֵר: "בָּרוּךְ מְשַׁנֶּה אֶת הַבְּרִיּוֹת". אֶת הַקִּטֵּעַ, וְאֶת הַסּוּמָא, וְאֶת פְּתוּיֵי הָרֹאשׁ, וְאֶת הַחִגֵּר, וְאֶת הַמּוּכֵּה שְׁחִין, וְאֶת הַבַּהֲקָנִים, אוֹמֵר: "בָּרוּךְ דַּיֵּין אֱמֶת"!

לָא קַשְׁיָא: הָא, מִמְּעֵי אִמּוֹ. הָא בָּתַר דְּאִיתְיְלִיד. דַּיְקָא נָמֵי, דְּקָתָנֵי דּוּמְיָא דְּקִטֵּעַ. שְׁמַע מִינַּהּ.

The gemara distinguishes between if a certain condition (בַּהֲקָנִים) is congenital or not with the ramification being the type of beracha one recites upon seeing a person afflicted with it. 

If one is born with it then the correct blessing is מְשַׁנֶּה הַבְּרִיּוֹת whereas if it develops afterwards then the suitable beracha is דַּיֵּין אֱמֶת. 

Presumably the peshat is that if one is born with it then it cannot be attributed to ones sins having caused it, with the prescribed beracha reflecting that, whereas if it pops up during a person's life then it is viewed as a divinely imposed judgement for some wrong committed (see משנה ברורה to siman 225 s"k 26 where he explains מברך דיין האמת – שבא לו זה ע"י עונש). 

Now, if one can be born with sins to correct and atone for from a previous life then even if it is congenital it can be deserved punishment with the BDE beracha relevant and applicable.

Once again, apparently, we see the Bavli not countenancing such a notion, with the congenital defect a product of HaShem's inscrutable will. 

(A counter-argument can be made that as it is unknown whether this condition is the result of sin or not, as perhaps this is a fresh soul, we therefore roll out this new blessing [it would resolve רע"א's safeik on the appropriate blessing when one is unsure if it congenital or not]. I would respond with 1) I believe the בעלי דעת הגלגול are of the opinion that most if not all souls after the initial fresh batch are recycled 2) even if new souls do occassionally descend part of the attraction of gilgul is solving for babies and children being hit with undeserved suffering with gilgul providing a neat explanation so if we're presented with a baby suffering from some freakish disorder it's to the contrary ever more compelling to assume that it is a manifestation of divine justice for misdemeanors committed in a previous incarnation 3) if it develops later in life too we can always be unsure if it is in response to sin or a product of Gods will, apparently we try to avoid positing the latter and prefer attributing it to sin wherever possible [unless one claims that post birth stuff only occur due to sin])