TL;DR: For certain types of scenarios (ie a murderer) Rabbinic courts would be able to carry out executions whenever the situation would arise... but they wouldn't kill via one of 4 methods of capital punihments, rather they'd kill via an "indirect" manner.
While the mishnah in Makkos (1:10) that you cited does state that "a court that executes one person in seven years/ seventy years is called 'destructive'"- this raises a potentially huge problem.
(some quick background)
In order for a person to get the death penalty, they need:
- 1) Two witnesses to explicitly warn the person the act in question violates the Torah and the punishment it carries (Rambam Hilchos Sanhedrin 12:2)
- 2) The action has to be committed "toch k'dai dibbor"/ ie a few seconds (ibid)
- 3) Two witnesses have to see the crime being committed (Rambam Hilchos Eidus 4:1)
... and all of this is BEFORE the extensive drisha v'chakira the witnesses will undergo in Beis Din.
Due to all these technicalities and logistics, it makes it absurdly complicated to satify all these conditions and administer the death penalty.
However- this can cause MAJOR problems
We've established that due to legalities/technicalities it's incredibly difficult to be administer the death penalty, but what about a person who's a serial killer-- who's shrewd, makes sure there are no witnesses for his killings etc; would the Sanhedrin really allow a person like that to freely roam around??
A: Of course not!
The Talmud in Sanhedrin 81b tells us about the concept of a "kippah"- a small chamber where they would bring such a person.
מתני׳ ההורג נפש שלא בעדים מכניסין אותו לכיפה ומאכילין אותו (ישעיהו ל, כ) לחם צר ומים לחץ:
MISHNA: one who kills a person not in the presence of witnesses [and it is impossible to judge him in court], the court places him into a vaulted (ie tiny) chamber and feeds him sparing bread and scant water (see Isaiah 30:20).
The Rambam (Hilchos Rotzeach 4:8) codifies what would happen:
הַהוֹרֵג נְפָשׁוֹת וְלֹא הָיוּ עֵדִים רוֹאִין אוֹתוֹ כְּאַחַת אֶלָּא רָאָהוּ הָאֶחָד אַחַר הָאֶחָד אוֹ שֶׁהָרַג בִּפְנֵי שְׁנֵי עֵדִים בְּלֹא הַתְרָאָה אוֹ שֶׁהֻכְחֲשׁוּ הָעֵדִים בִּבְדִיקוֹת וְלֹא הֻכְחֲשׁוּ בַּחֲקִירוֹת. כָּל אֵלּוּ הָרַצְחָנִים כּוֹנְסִין אוֹתָן לְכִפָּה וּמַאֲכִילִין אוֹתָן לֶחֶם צַר וּמַיִם לַחַץ עַד שֶׁיָּצֵרוּ מֵעֵיהֶן וְאַחַר כָּךְ מַאֲכִילִין אוֹתָן שְׂעוֹרִים עַד שֶׁתִּבָּקַע כְּרֵסָם מִכֹּבֶד הַחלִי:
Someone who commits a murder and the witnesses didn't the see the testimony as one, or if he killed in front of two witnesses but he wasn't warned, or the witnesses were "weakened" via the examining questions but not the investigation. All of these murderers they would bring to a kippah and feed him a small amount bread and scant water until his intestines contract and then the court feeds him barley that expands in his innards until his stomach explodes.
Bottom Line: Beis Din would still technically kill such a person, but they would do so "indirectly".