Because docutils is just terrible...

RstTableReformatter.java

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

public class RstTableReformatter {
  public static void main(String[] args) {
    Table table = parse("Your table here");
    System.out.println(print(table));
  }

  public static class Table {
    public Row header;
    public List<Row> body;
  }

  public static class Row {
    public String[] entries;
  }

  public static Table parse(String string) {
    Table table = new Table();
    table.body = new ArrayList<>();
    String[] tableLines = string.lines().toArray(String[]::new);
    boolean seenHeader = false;
    Row current = null;
    for (String line : tableLines) {
      if (line.startsWith("+")) {
        if (current != null) {
          if (seenHeader) {
            table.body.add(current);
          } else {
            table.header = current;
          }
          current = null;
        }
        if (line.startsWith("+=")) {
          seenHeader = true;
        }
        continue;
      }
      if (line.startsWith("|")) {
        String[] array = Arrays.stream(line.split("\\|")).skip(1).map(String::strip).toArray(String[]::new);
        if (current == null) {
          current = new Row();
          current.entries = array;
        } else {
          for (int i = 0; i < array.length; i++) {
            current.entries[i] += " " + array[i];
          }
        }
      }
    }
    return table;
  }

  public static String print(Table table) {
    int columns = table.header.entries.length;
    int[] widths = new int[columns];
    String[] entries = table.header.entries;
    for (int i = 0; i < entries.length; i++) {
      widths[i] = entries[i].length();
    }
    for (Row row : table.body) {
      for (int i = 0; i < row.entries.length; i++) {
        widths[i] = Math.max(widths[i], row.entries[i].length());
      }
    }
    for (int i = 0; i < widths.length; i++) {
      widths[i] = widths[i] + 2; // leading and trailing space
    }
    StringBuilder sb = new StringBuilder();
    for (int width : widths) {
      sb.append("+");
      sb.append("-".repeat(Math.max(0, width)));
    }
    sb.append("+\n");

    sb.append("|");
    for (int i = 0; i < table.header.entries.length; i++) {
      sb.append(" ");
      sb.append(table.header.entries[i]);
      sb.append(" ".repeat(Math.max(0, widths[i] - table.header.entries[i].length() - 1)));
      sb.append("|");
    }
    sb.append("\n");
    for (int width : widths) {
      sb.append("+");
      sb.append("=".repeat(Math.max(0, width)));
    }
    sb.append("+\n");

    for (Row row : table.body) {
      sb.append("|");
      for (int i = 0; i < row.entries.length; i++) {
        sb.append(" ");
        sb.append(row.entries[i]);
        sb.append(" ".repeat(Math.max(0, widths[i] - row.entries[i].length() - 1)));
        sb.append("|");
      }
      sb.append("\n");
      sb.append("+");
      for (int width : widths) {
        sb.append("-".repeat(Math.max(0, width)));
        sb.append("+");
      }
      sb.append("\n");
    }

    return sb.toString();
  }
}